https://chemwiki.ch.ic.ac.uk/api.php?action=feedcontributions&feedformat=atom&user=Bb406 2026-04-06T09:15:27Z User contributions MediaWiki 1.43.0 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb406&diff=38318 2009-01-27T17:56:32Z

<p>Bb406: Undo revision 38315 by Jrb06 (Talk)</p> <hr /> <div>&lt;P&gt;&lt;B&gt;Birendra Balakrishnan&lt;/B&gt; <br /> &lt;/P&gt;<br /> =Structure &amp; Spectroscopy=<br /> ==The Hydrogenation of Cyclopentadiene Dimer== <br /> <br /> An analysis was carried out on the energy contribution of<br /> strecthing (str), bending (bnd), torsion (tor), van der Waals (vdw)<br /> and H-bonding (H-bond) on the endo (Fig. 1) and exo (Fig. 2) dimers<br /> of cyclopentadiene. Further investigation was taken into the<br /> hydrogenated forms of the endo dimer (Fig. 3) (Fig. 4).<br /> <br /> When cyclopentadiene dimerises it preferentially produces the endo dimer over the exo dimer. Subsequent hydrogenation of the endo dimer initially gives one of the dihydro derivatives. On continued hydrogenation the tetrahydro derivative is formed.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Exo Dimer (1)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Endo Dimer (2)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogenated Endo Dimer (3)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogenated Endo Dimer (4)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:mol1.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol2.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol3.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol4.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 1.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule_2.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 4.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> Using the MM2 modelling technique, the geometries and energies for all four molecules were calculated.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;Energies (kcal/mol)&lt;BR&gt;<br /> &lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Exo Dimer (1)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Endo Dimer (2)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogenated Endo Dimer (3)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogenated Endo Dimer (4)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Stretch&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.9962&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.9757&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.0151&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.9158 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.5727&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.6608&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.9050&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;15.4671 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Str-Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-0.7501&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-0.7374&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-0.6532&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-0.4740 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Torsion&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;8.4461&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;10.6446&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.2630&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.6539 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Non 1,4 VdwW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-1.9836&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-2.2530&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-1.3458&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-1.1543 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;1,4 VdW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.3674&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.6964&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6.8202&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.7185 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Dipole-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.3770&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.4557&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.1638&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.1403 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;TOTAL&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;35.0258&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;37.4428&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;40.1681&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;35.2672 <br /> &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> &lt;P STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;<br /> <br /> As the lowest in energy, the exo dimer is the most thermodynamically stable. As such it would be expected to be the major product. However, as the endo dimer dominates it is a fair to assume this dimer is the kinetic product. The reaction is kinetically controlled with the endo intermediate formed during the reaction being lower in energy than the exo intermediate.<br /> <br /> The hydrogenated endo dimer ,4, is lower in energy than the other hydrogenated product ,3. The hydrogenation of dicyclopentadiene is a thermodynamically controlled process. Therefore, the more thermodynamically stable product predominates. The rate of reaction is dependent on the rate of diffusion of hydrogen onto the reagent molecule. Molecule 4 allows faster diffusion of hydrogen than its counterpart.<br /> <br /> On closer comparison of the relative contributions of total energy by different modes of motion and interactions, it became apparent that bending strain in molecule 4 was lower than that in molecule 3 (approximately 48% lower). This is due to the double bond in molecule 4 being under less strain. All other interactions were relatively comparable.<br /> <br /> ==Stereochemistry of Nucleophilic additions to a pyridinium ring (NAD+ analogue)==<br /> <br /> ===Alkylation of prolinol===<br /> <br /> An optically active derivative was reacted with a Grignard reagent, methyl magnesium iodide, to alkylate the pyridine ring on the fourth position.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent (5)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product (6)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:mol5.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol6.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 5.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule_6.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> Using the MM2 modelling technique, the geometries and energies were calculated.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;Energies (kcal/mol)&lt;BR&gt;<br /> &lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent (5)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product (6)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Stretch&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.1863&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.4771&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;11.3802&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;14.5694&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Str-Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.0495&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.1630&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Torsion&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.0797&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.4644&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Non 1,4 VdwW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-2.0057&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-2.0224&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;1,4 VdW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;11.8968&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.3054&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Dipole-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-3.9662&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-4.0628&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Charge-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.7003&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;---&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;TOTAL&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;26.3208&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;28.8942&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> &lt;P STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;<br /> <br /> The carbonyl group, of the reagent, is not coplanar with the aromatic ring system. The carbonyl group is angled away from the plane of the pyridine ring, anti to the chiral hydrogen. The expected dihedral angle in a perfectly planar system is 0, whereas in this molecule the angle is 24.3975.<br /> <br /> The product is higher in energy than that of the reagent. This is possibly due to the loss of aromaticity from the pyridine system.<br /> <br /> ====Mechanistic Control====<br /> <br /> Methyl magnesium iodide reacts as a methyl carbanion and magnesium iodide cation.<br /> <br /> <br /> [[Image:Mol5-6rec.gif]]<br /> <br /> <br /> The reaction is stereo-specific as the methyl carbanion is delivered to the top face of the molecule. This is a result of coordination of the magnesium iodide cation with the amide oxygen atom. Conjugate delivery of the methyl ligand from magnesium to the carbon attacked would generate the magnesium enolate.<br /> <br /> Improvements can be made to the model if factors such as activation barriers and the energies of transition states were included. These aspects of the reaction would provide more information on which to provide a more comprehensive analysis. Furthermore, analysis on thermodynamic or kinetic control can be made.<br /> <br /> ===Nucleophilic Addition of NHPh===<br /> <br /> This is another example of stereo control of a reaction.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent (7)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product (8)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:mol7.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol8.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 7.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule_8.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> Using the MM2 modelling technique, the geometries and energies were calculated.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;Energies (kcal/mol)&lt;BR&gt;<br /> &lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent (7)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product (8)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Stretch&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.7056&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.8980&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.2918&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.5500&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Str-Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.3846&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.6436&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Torsion&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-5.7456&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-11.6096&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Non 1,4 VdwW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-1.1902&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-2.3155&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;1,4 VdW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.4066&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;20.6211&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Dipole-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-4.7586&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-4.8676&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Charge-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.5603&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;---&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;TOTAL&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.6545&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.9200&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> &lt;P STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;<br /> <br /> The amide carbonyl group of the reagent points down from the plane of the aromatic system. The dihedral angle between this group and the ring is 42.5706.<br /> <br /> The NHPh group attacks from the top face of the molecule in order to avoid electronic repulsion between the attacking phenyl group and the amide carbonyl. To this end, the NHPh group attacks from the top face and points upward, anti to the carbonyl.<br /> <br /> ==Stereochemistry &amp; Reactivity of an Intermediate in the synthesis of Taxol==<br /> <br /> Taxol is an important drug in the treatment of ovarian cancer. Proposed by Paquette, the initial synthesis of the intermediate has the carbonyl group pointing either up or down. <br /> <br /> While standing, the intermediate isomerises to the alternative carbonyl isomer. This type of isomerism is known as atropisomerism.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intermediate (10)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intermediate (11)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:mol10.GIF]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol11.GIF]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 10.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule_11.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> Using the MM2 modelling technique the relative energies were calculated.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;Energies (kcal/mol)&lt;BR&gt;<br /> &lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intermediate (10)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intermediate (11)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Stretch&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.8191&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.6015&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.4262&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.5803&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Str-Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.4568&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.3410&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Torsion&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.3581&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0663&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Non 1,4 VdwW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-0.8530&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-0.8134&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;1,4 VdW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;14.0263&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.5761&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Dipole-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.1366&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.2598&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;TOTAL&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;54.3702&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;50.6116&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> &lt;P STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;<br /> <br /> Intermediate 11 is energetically more stable than Intermediate 10. However, the difference in energies is small providing favourable conditions for the isomerism between the two forms. Intermediate 11 is a hyperstable olefin due to the larger ring size and the stability provided by the caged structure of the olefin and the strain of the parent polycycloalkane.<br /> <br /> Through minor adjustments, the energy of the intermediate was lowered. However, the energy minimisation process would often revert the structure to a previous iteration unavoidably. There are substantial difficulties in using such a modelling technique.<br /> <br /> ==Room Temperature Hydrolysis of a Peptide==<br /> <br /> By using careful conformational anaylsis, it is possible to understand the mechanistic control of a reaction by two isomers. The two isomers are structurally very similar, but have very different rates of reaction.<br /> <br /> Firstly, anaylsis was carried out on the cis isomer.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 13 (Axial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 13 (Equitorial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product 13&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol13a.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol13e.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol13p.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 13A.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule_13E.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 13P.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> Using the MM2 modelling technique, the geometries and energies for all four molecules were calculated.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;Energies (kcal/mol)&lt;BR&gt;<br /> &lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 13 (Axial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 13 (Equitorial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product 13&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Stretch&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.4093&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.9333&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.2373&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.8455&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.4342&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;8.0489&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Str-Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.5890&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.5900&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.6174&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Torsion&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;11.5518&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;9.0388&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6.1829&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Non 1,4 VdwW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-8.1596&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-4.6424&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-3.3109&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;1,4 VdW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;10.4828&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;10.1843&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;14.9312&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Dipole-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-4.4289&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-3.0162&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;4.2989&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;TOTAL&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.2898&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.5219&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;32.0056&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> &lt;P STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;<br /> <br /> The trans isomer was then studied.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 14 (Axial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 14 (Equitorial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product 14&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol14a.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol14e.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Mol14p.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 14A.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule_14E.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;Exo Dimer&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;Molecule 14P.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> Using the MM2 modelling technique, the geometries and energies for all four molecules were calculated.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;Energies (kcal/mol)&lt;BR&gt;<br /> &lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 14 (Axial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Reagent 14 (Equitorial)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Product 14&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Stretch&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.5415&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.4521&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.2525&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;5.5936&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.6417&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6.4188&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Str-Bend&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.5768&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.4964&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.5666&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Torsion&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;9.9304&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;8.0389&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;4.1882&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Non 1,4 VdwW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-6.5075&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-7.6863&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-3.5266&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;1,4 VdW&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;9.7592&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;9.9793&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;15.2661&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;Dipole-Dipole&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-1.5419&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-6.1448&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;4.5363&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=138&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;B&gt;TOTAL&lt;/B&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.3521&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;9.7772&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;28.7019&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> &lt;P STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;<br /> <br /> ====Mechanistic Control====<br /> <br /> In order to react successfully, the hydroxy oxygen has to approach the carbonyl group in a strict orientation. A successful hydrolysis needs the oxygen lone pair to have the best overlap with the C=O π* orbital. This involves approaching in line with the C=O bond and at an elevation of 108 degrees.<br /> <br /> The cis isomer has two further isomers, where the group attached to the nitrogen is either axial or equitorial to the ring. The axial isomer provides the best approach to hydrolyise the peptide group. However, energetically it is very similar to the equitorial isomer. This means that there is a very small barrier for isomeric conversion. This allows the equitorial isomer to react readily via the axial isomer.<br /> <br /> As with the cis isomer; the trans isomer has axial and equitorial conformations. However, in this case the two differ in energy greatly. The reactive conformation is axial, though due to the special stability of trans decalin the most stable is the equitorial conformation. This conformation suffers least from diaxial interactions. The energy barrier between the conformations means that the equilibrium between the axial and equitorial conformations is strongly favoured to the equitorial.<br /> <br /> The result is that the cis form is much more reactive than the trans form.<br /> <br /> ==Regioselective Addition of Dichlorocarbene==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;HOMO&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;HOMO -1&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;HOMO -2&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Homo.jpg|200px]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Homom1.jpg|200px]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Homom2.jpg|200px]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LUMO&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LUMO +1&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LUMO +2&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Lumo.jpg|200px]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Lumop1.jpg|200px]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:Lumop2.jpg|200px]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28264 2008-12-02T12:52:29Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||600px|]] <br /> <br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> The optimisation provides the following data:<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Mo-P Bond&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.029Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.426Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Mo-C Bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.029Å, 2.029Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.037Å, 2.041Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;P-Mo-P Angle (Degrees)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;180.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;176.7&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;R-P-Mo (Degrees)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;117.09, 117.06, 115.68&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;121.02, 120.52, 111.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Cis Isomer===<br /> <br /> The Cis Isomer<br /> <br /> [[Image:CIso.jpg||600px|]] <br /> <br /> [[Image:CIR.jpg|thumb|400px|Cis Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;9.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6:15:21.6&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> The optimisation provides the following data:<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Mo-P Bond&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.648Å, 2.648Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.525Å, 2.533Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Mo-C Bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.982Å, 1.982Å, 2.033Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.981Å, 1.983Å, 2.034Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;P-Mo-P Angle (Degrees)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;92.9&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;94.8&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;R-P-Mo (Degrees)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;113.90, 118.26, 118.54&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;112.9, 114.9, 121.1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28263 2008-12-02T12:46:42Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||600px|]] <br /> <br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> The optimisation provides the following data:<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Mo-P Bond&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.029Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.426Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Mo-C Bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.029Å, 2.029Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.037Å, 2.041Å&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;P-Mo-P Angle (Degrees)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;180.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;176.7&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;R-P-Mo (Degrees)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;117.09, 117.06, 115.68&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;121.02, 120.52, 111.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28262 2008-12-02T12:41:38Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||600px|]] <br /> <br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The optimisation provides the following data:<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Optimised Calculation&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Literature Value&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28255 2008-12-02T12:37:24Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||600px|]] <br /> <br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28254 2008-12-02T12:35:35Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||600px|]] [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28253 2008-12-02T12:35:16Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||400px|]] [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28252 2008-12-02T12:35:01Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||400px|]]<br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28251 2008-12-02T12:34:39Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg||400px|]]<br /> <br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28250 2008-12-02T12:33:44Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg]]<br /> <br /> [[Image:TIR.jpg|thumb|400px|Trans Spectra ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28249 2008-12-02T12:33:15Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg]]<br /> <br /> [[Image:TIR.jpg|thumb|200px| ]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28248 2008-12-02T12:31:48Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> The Trans Isomer<br /> <br /> [[Image:TIso.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:TIR.jpg&diff=28247 2008-12-02T12:30:48Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:TIso.jpg&diff=28246 2008-12-02T12:30:27Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:CIso.jpg&diff=28245 2008-12-02T12:29:48Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:CIR.jpg&diff=28244 2008-12-02T12:29:39Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28243 2008-12-02T12:26:26Z

<p>Bb406: /* Trans Isomer */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2DZ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-773.36&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (h)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3:32:42.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28242 2008-12-02T12:24:25Z

<p>Bb406: /* Transition Metal Complex */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.<br /> <br /> ===Trans Isomer===</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28241 2008-12-02T12:20:23Z

<p>Bb406: /* Transition Metal Complex */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.<br /> <br /> The structure is much more complex than the previous examples, and as such requires extra effort to optimise. Initially a RB3LYP calculation is completed using the LANL2MB basis set. Then further optimisation using the LANL2-DZ basis set.</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28240 2008-12-02T12:17:17Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.<br /> <br /> ==Transition Metal Complex==<br /> <br /> In this investigation, a transition metal complex will be analysed via its vibrational frequency data. The cis and trans isomers of the Mo(CO)&lt;sub&gt;4&lt;/sub&gt;(PMe&lt;sub&gt;3&lt;/sub&gt;)&lt;sub&gt;2&lt;/sub&gt;complex will be examined.</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28239 2008-12-02T12:10:09Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> With a single negative frequency value, the structure is a transition state.</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28238 2008-12-02T12:09:06Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C3V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28237 2008-12-02T12:08:48Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate in-time with each other; Remaining Hydrogen out-of-time&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;19.60&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3854.27&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;'/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3653.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;55.98&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1640.59&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;849.113&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-318.05&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28235 2008-12-02T12:02:49Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:HIR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN1.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN2.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN3.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN4.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN5.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:HN6.jpg ]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

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<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28227 2008-12-02T11:57:22Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> The results have all positive frequencies showing a ground state structure.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (D3H Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28226 2008-12-02T11:55:17Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28225 2008-12-02T11:54:53Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> [[Image:NH3IR.jpg]]<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3IR.jpg&diff=28224 2008-12-02T11:54:08Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28223 2008-12-02T11:53:56Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28222 2008-12-02T11:51:09Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:NH3v6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3v6.jpg&diff=28221 2008-12-02T11:50:00Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3v5.jpg&diff=28220 2008-12-02T11:49:53Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3v4.jpg&diff=28219 2008-12-02T11:49:47Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3v3.jpg&diff=28218 2008-12-02T11:49:40Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3v2.jpg&diff=28217 2008-12-02T11:49:32Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=File:NH3v1.jpg&diff=28216 2008-12-02T11:49:24Z

<p>Bb406: </p> <hr /> <div></div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28215 2008-12-02T11:48:45Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (C3V Symmetry) Vibrational Analysis===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two Hydrogen atoms oscillate out-of-time with each other; Remaining Hydrogen stationary&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;7.09&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3775.76&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Asymmetric Stretch E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two hydrogen atoms oscillate together and the other out-of-time along the bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.07&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3575.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Hydrogen atoms oscillate in time along N-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.72&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl oscillates in plane side-to-side&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;41.73&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1680.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend E&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two N-H bonds scissor in plane; Remaining B-Cl still&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;599.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;452.30&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Nitrogen oscillates perpendicular to the plane&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28214 2008-12-02T11:32:34Z

<p>Bb406: /* Vibrational Analysis */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28213 2008-12-02T11:32:05Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> On inspection of all optimisation results; the RB3LYP method provides the lowest energy with the long bond structure. However, the variance between all the energy figures is insignificant.<br /> <br /> The barrier to inversion is calculated by taking the difference in energy between the C3V and D3H forms. <br /> <br /> By taking the values from the above optimisations, the barrier to conversion was calculated to be 19.21 kJmol&lt;sup&gt;-1&lt;/sup&gt;. This is comparable to the literature value of 24.3 kJmol&lt;sup&gt;-1&lt;/sup&gt;.<br /> <br /> <br /> ===Vibrational Analysis===</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28212 2008-12-02T10:52:14Z

<p>Bb406: /* NH3 (RMP2-FU High Symmetry) Optimisation Calculation */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28211 2008-12-02T10:51:51Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH3 (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28210 2008-12-02T10:51:33Z

<p>Bb406: /* NH&lt;sub&gt;3&lt;/sub&gt; */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (Long Bond) Optimisation Calculation===<br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH3 (RMP2-FU High Symmetry) Optimisation Calculation===<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

Bb406 https://chemwiki.ch.ic.ac.uk/index.php?title=Rep:Mod:bb407&diff=28209 2008-12-02T10:48:43Z

<p>Bb406: /* NH3 (High Symmetry) Optimisation Calculation */</p> <hr /> <div>=Inorganic Computational Chemistry Lab=<br /> <br /> ==Vibrational Analysis==<br /> <br /> Vibrational analysis calculations are a function of the potential energy surface (PES) with respect to equilibrium geometry's bond length. The particular function used is a second derivative.<br /> <br /> Using this calculation, the output provided information regarding the optimised structure. The optimisation can give an indication of whether the ground or transitional states are most stable. The output also allows for the analysis of the structure's vibrational frequencies.<br /> <br /> By analysing the vibrational frequencies, information on the structure can be deduced. Positive frequencies throughout the output data indicate an optimised geometry in the ground state. A single negative frequency in amongst the positive, is an indication of a transitional state. Multiple negative frequencies means that the molecular structure needs further optimisation.<br /> <br /> In the following exercise, the optimisation must take place prior to vibrational analysis. The model used was the RB3LYP calculation. A basis set has to be used in conjunction with the calculation. The basis set that was chosen was the LANL2MB. This set was used as the calculations involve optimising a molecular structure that contains chlorine.<br /> <br /> As a second row atom, chlorine needed the more complex basis set to accomodate its electronic structure.<br /> <br /> ==BCl&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3Pic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;BCL3&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;BCL3.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.87&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;120&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;LANL2MB&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-69.44&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;17.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===BCl&lt;sub&gt;3&lt;/sub&gt; Vibrational Analysis===<br /> <br /> <br /> [[Image:BCL3IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: D3H&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates along B-Cl bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;258.67&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;939.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;417.38&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Chlorine atoms oscillate in time along B-Cl bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib4.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;43.78&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;376.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;2&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Boron oscillates perpendicular to plane of molecule; Slight movement of Chlorine atoms&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib5.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Two B-Cl bonds scissor in plane; Remaining B-Cl oscillates along bond&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:BCL3vib6.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3.94&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;214.13&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Bend E'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Single B-Cl oscillates in plane of molecule&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6. Simple spectroscopic theory provides the rationale to interpret the data. Dipole moments provide the activity in infra-red spectroscopy. The symmetric A&lt;sub&gt;1&lt;/sub&gt;' stretch produces no change in dipole moment, and as a result is inactive.<br /> <br /> Degenerate E' sets have a difference as a result of variance between strecthing and bending. The B-Cl bending vibration is located at 214.13 cm&lt;sup&gt;-1&lt;/sup&gt;; B-Cl stretch vibrations at 939.47 cm&lt;sup&gt;-1&lt;/sup&gt;. The intensity difference again correlates to stretching having a greater change than the bending vibrations.<br /> <br /> ==H&lt;sub&gt;2&lt;/sub&gt;O==<br /> <br /> For the optimisation of this molecule, which is composed of much simpler component atoms than BCl3, the 3-21G basis set was used in conjunction with the RB3LYP method. A simpler basis set is sufficient to adequately model the electronic structure.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3D Representation&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2OPic.gif]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;&lt;jmol&gt;&lt;jmolApplet&gt;&lt;title&gt;H2O&lt;/title&gt;&lt;color&gt;white&lt;/color&gt;<br /> &lt;size&gt;150&lt;/size&gt;&lt;script&gt;zoom 200; cpk -20;&lt;/script&gt;<br /> &lt;uploadedFileContents&gt;H20.mol&lt;/uploadedFileContents&gt;<br /> &lt;/jmolApplet&gt;&lt;/jmol&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> <br /> ===Optimised Structure===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;B-Cl Distance (Å)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bond Angle (Degrees)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;104.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;21.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===Frequency Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FREQ&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3-21G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-75.97&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2.24&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C2V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (s)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;16.0&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> ===H&lt;sub&gt;2&lt;/sub&gt;O Vibrational Analysis===<br /> <br /> <br /> [[Image:H20IR.jpg]]<br /> <br /> <br /> The data provides an IR spectra from which further anaysis was made.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Diagram&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Intensity&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Frequency (cm&lt;sup&gt;-1&lt;/sup&gt;)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Symmetry: C2V&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Vibration Desciption&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib1.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.56&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3553.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch B&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate out-of-time to each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib2.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;13.71&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;3412.40&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Assymmetric Stretch A&lt;sub&gt;1&lt;/sub&gt;&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Oxygens oscillate in-time with each other along O-H bonds&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;[[Image:H2Ovib3.jpg]]&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;36.74&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1692.47&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Bend A&lt;sub&gt;1&lt;/sub&gt;'&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;O-H bonds move in a scissoring action &lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> On inspection of the data it is apparent that the vibrational frequencies are all positive. This means that the molecule is at a ground state. The mathematical implication is that the molecule has reached a nadir for the bond length with respect to PES.<br /> <br /> As expected, the molecule has the correct number of vibrational frequencies. This is based on the vibrational modes afforded to non-linear molecules; 3n-6.<br /> <br /> <br /> ==BH&lt;sub&gt;3&lt;/sub&gt; Molecular Orbital Analysis==<br /> <br /> Using Gaussview a Molecular Orbital (MO) diagram was put together. The example used was BH&lt;sub&gt;3&lt;/sub&gt;, which was covered during previous lecture courses.<br /> <br /> [[Image:BH3MO.gif]]<br /> <br /> The MO diagram produced is very helpful in providing a qualitative arguement for reactivity. In order for BH&lt;sub&gt;3&lt;/sub&gt; to complete its octet, it requires two more electrons. It is a well known fact that BH&lt;sub&gt;3&lt;/sub&gt; is lewis acidic. The a2&quot; orbital shows that the MO occupies a large and broad area above and below the plane of the molecule, allowing for easy attack from a lewis base. <br /> <br /> Interestingly, Gaussview predicted four filled MOs. However, the omitted MO was significantly lower in energy and so left out on the basis that this was an artefact of the prediction process.<br /> <br /> <br /> ==NH&lt;sub&gt;3&lt;/sub&gt;==<br /> <br /> In this section, ammonia is to be studied as it possesses the ability to tunnel between PES minima. This means that the structure can invert in a process that superficially is not dissimilar to the inversion on Sn2 centres. This provides two equivalent mirror states with C3V symmetry and a transition state with D3H.<br /> <br /> To investigate further the RB3LYP calculation was used again in conjunction with the 6-31G basis set.<br /> <br /> ===NH3 Optimisation Calculation===<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.32&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1:14&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH3 (Long Bond) Optimisation Calculation===<br /> <br /> In order to perform this optimisation, symmetry was ignored while one of the N-H bonds was given a set distance of 1.01Å.<br /> <br /> This produces a variance in symmetry and in the computing time that was required. The energy difference between the long bond optimisation and the normal optimisation is insignificant.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.34&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C1&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;2:20&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> There was a significant increase in calculation time. This has been attributed to the methods by which Gaussview runs the calculation. Without the symmetry elements the calculations take longer as the program cannot use symmetry to 'shortcut' the process.<br /> <br /> <br /> ===NH&lt;sub&gt;3&lt;/sub&gt; (High Symmetry) Optimisation Calculation===<br /> <br /> By using another atom as a 'dummy' the geometry of the molecular structure is forced to maintain a specific chosen shape.<br /> <br /> The structure is now in D3H symmetry, explaining the speedy calculation time.<br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;FOPT&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RB3LYP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-31G&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.53&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0.00&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;D3H&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:31&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;<br /> <br /> <br /> ===NH3 (RMP2-FU) Optimisation Calculation===<br /> <br /> In the following optimisation calculations the RMP2-FU method was used in conjunction with the 6-311+G(d,p) basis set. The method and basis set should provide a better calculation.<br /> <br /> <br /> &lt;P ALIGN=CENTER STYLE=&quot;margin-bottom: 0cm&quot;&gt;&lt;BR&gt;<br /> &lt;/P&gt;&lt;TABLE WIDTH=585 BORDER=1 BORDERCOLOR=&quot;#000000&quot; CELLPADDING=4 CELLSPACING=0&gt;<br /> <br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;File Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;.log&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Type&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;SP&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Calculation Method&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;RMP2-FU&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Basis Set&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;6-311+G(d,p)&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Energy (a.u.)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;-56.43&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Dipole Moment (D)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;1.66&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Point Group&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;C3V&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;TR&gt;<br /> &lt;TH WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;Time (min)&lt;/P&gt;<br /> &lt;/TH&gt;<br /> &lt;TD WIDTH=101&gt;<br /> &lt;P ALIGN=CENTER&gt;0:16&lt;/P&gt;<br /> &lt;/TD&gt;<br /> &lt;/TR&gt;<br /> &lt;/TABLE&gt;</div>

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