ChemWiki - User contributions [en]

I love MO's

2018-05-25T16:58:41Z

Jw4116: /* Please Mark this wikiː https://wiki.ch.ic.ac.uk/wiki/index.php?title=Jw4116_Y2_inorg-comp */

=INAPPROPRIATE NAME ACCIDENTALLY SUBMITTED=

==PLEASE MARK THIS WIKIː https://wiki.ch.ic.ac.uk/wiki/index.php?title=Jw4116_Y2_inorg-comp==

I love MO's

2018-05-25T16:58:16Z

Jw4116: Created page with "=INAPPROPRIATE NAME ACCIDENTALLY SUBMITTED= ==Please Mark this wikiː https://wiki.ch.ic.ac.uk/wiki/index.php?title=Jw4116_Y2_inorg-comp=="

=INAPPROPRIATE NAME ACCIDENTALLY SUBMITTED=

==Please Mark this wikiː https://wiki.ch.ic.ac.uk/wiki/index.php?title=Jw4116_Y2_inorg-comp==

Jw4116 Y2 inorg-comp

2018-05-25T16:56:06Z

Jw4116:

=PART 1=

==BH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
Predicted change in Energy=-4.343399D-10
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0054 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity

ǃMode
|-
|1
|A2''
|1163
|93
|out-of-plane bend
|-
|2, 3
|x2 E'
|1213
|14
|bend
|-
|4
|A1'
|2582
|0
|symmetric stretch
|-
|5, 6
|x2 E'
|2715
|126
|aymmetric stretch
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|500px]]

MO diagram source <ref>http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>

==NH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
Predicted change in Energy=-7.830784D-11
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- -11.5222 -11.4865 -0.0028 0.0246 0.1415 25.6160
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
Predicted change in Energy=-2.028053D-07
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 0.0007 0.0007 0.0011 19.0877 23.7564 42.9908
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEformation(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1 = -ΔEdissociation

Analysisː The bond energy value calculated is in the rough ballpark for normal bond energies (b.t.w 200-500kJ.mol-1) however, as it is a dative bond formed from a Lewis acid/base pair it will be weaker (lower energy) than a traditional covalent bond in which an electron is donated by each atom. This logic correlates with the value calculated.

==BBr3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)LANL2DZ

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
Predicted change in Energy=-8.610617D-10
</pre>

BBr3 [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

=PART 2=

==Benzene==

[[File: SummarytableBenzeneJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000199 0.000450 YES
RMS Force 0.000081 0.000300 YES
Maximum Displacement 0.000847 0.001800 YES
RMS Displacement 0.000299 0.001200 YES
Predicted change in Energy=-4.636845D-07
</pre>

Benzene [[Media: JW BENZENE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BENZENE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Borazine==

[[File: SummarytableBorazineJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000086 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.359581D-08
</pre>

Borazine [[Media: JW BORAZINE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BORAZINE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Analysis==

{| class="wikitable"
|+
|-
! Charge Distribution
! Atom (Pauling E.N)ː Gaussian Value
! Explanation
|-
|[[File: Charge-borazineJW4116.PNG|200px]]
|N (3.04)ː -1.102

B (2.04)ː 0.747

H-N (2.20)ː 0.432/ H-B (2.20)ː -0.077
|As shown in the picture and from general intuition from the knowledge of relative electronegativites, the charge distribution in borazine is very uneven. This is due to different hetero atoms having a exposed positive charge from the nucleus, increasing their ability to attract electron density from those atoms with a looser hold on their electrons. Although there is an uneven distribution of charge within the molecule, due to the symmetric distribution in charge, the molecule remains neutral with no single molecular dipole moment (they cancel out). The uneven distribution also results in a more reactive aromatic species as charges can attract nucleo/electrophillic species increasing the probability of a reaction (Nː nucleophillic, Bː electrophillic). Also half the protons would be more acidic than the other half based on their affinity to negative charge.
|-
|[[File: Charge-benzene.PNG|200px]]
|C (2.55)ː -0.239

H-C (2.20)ː 0.239

|Due to the higher symmetry of the benzene molecule (lack of heteroatoms) the charge distribution is even between each atom (H and C). As shown in the picture, the amount of charge on each atom is determined by their relative electronegativity and ability to attract electron density from the covalent bond. The symmetrical and even distribution in charge results in a very stable aromatic compound; however, the increased negative charge around the carbon atoms increases its imperceptibility to attack from strong electrophiles (seen in experiments).
|-
|}

==Comparing MOs==

{| class="wikitable"
|+
|-
! Benzene MO (no.)
! Borazine MO (no.)
! Comparison
|-
|[[File: MO14benzenejw4116.jpg|200px]]
|[[File: MO15borazinejw4116.jpg|200px]]
|These MOs are very similar in shape and nodal/ phase distribution. Due to the relative electronegativity, there is a slight distortion of electron density towards the nitrogen. However, due to the σ-nature of the MO, the distortion is much less due to the effectiveness of the overlap and rigidity of the MO. The contributing p-orbitals all lie in the same plane, perpendicular to the principle axis.
|-
|[[File: MO17benzenejw4116.jpg|200px]]
|[[File: MO17borazinejw4116.jpg|200px]]
|As with MO14/15 the shapes of these MOs are very similar with the same nodal/ phase distribution and roughly the same shape. The difference in electronegativity and distribution of electron density is demonstrated by the reduction in symmetry from Benzene (D6h) to Borazine (D3h) as the electrons favour the N atom. This is a much more significant effect than the previous MO comparison due to the relative high diffusivity of π orbitals compared to σ.
|-
|[[File: MO19benzenejw4116.jpg|200px]]
|[[File: MO18borazinejw4116.jpg|200px]]
|These wacky looking orbitals are also very similar but, like the other examples, have varied symmetry due to the distortion in electron density from the polarized bonds in the heteroaromatic ring. The effects of being bonded to electronegative atoms is seen in the contributions from the H1s orbitals to the MO. The hydrogens bonded to the nitrogen contribute significantly lower to the overall structure relative to those bonded to the boron atoms.
|-
|}

==Aromaticity==

Aromaticity is a very important concept in chemistry which relates to cyclic molecules and electron delocalisation. Aromatic compounds tend to be much less reactive than their more saturated counterparts due to the inherent stability associated with even electron distribution and delocalisation. A pioneer in the field of aromaticity was Hückel who devised a system/set of rules which determines the aromatic nature of a vast number of molecules. The rules require the molecule to have: 4n+2 π-electrons, be planar and have a connected system of delocalised p-orbitals along the principle axis of the molecule (perpendicular to the plane of the molecule). The classic aromatic molecule is benzene and its aromatic nature was first considered when the enthalpy of hydrogenation of poly-saturated cyclic hydrocarbons was studied; this confirmed that benzene was far more stable than expected which lead to the introduction of aromatic theory which was backed up by IR analysis. The effect of delocalisation and resulting ring current is seen in 1HNMR due to the induced magnetic field generated by the electrons whizzing around the pi system.

Nowadays, due to our more advanced analytical techniques, we have confirmed that a planar molecule with a system of delocalised electrons in a π MO is not a complete picture in describing the full extent/ nature and possible contributions leading to aromatic properties. One example would be the influence of σ-delocalised MOs (as seen in MO 14/15 above) which arises from the p-orbitals lying along the plane of the molecule. The electrons in this MO are clearly delocalised due to the nodal planes dissecting the nuclei rather than being inbetween them. The resulting MO is also lower in energy (more stable) than the π delocalised orbital due to the more effective σ overlap.<ref>Kovačević, Borislav, et al. "The origin of aromaticity: Important role of the sigma framework in benzene." ChemPhysChem 5.9 (2004): 1352-1364.</ref> Other examples of aromatic compounds that break Hückels rules exist which display delocalised electrons and aromatic properties such as saturated inorganic rings (SiH2)n and (GeH2)n and a variety of others molecules.<ref>Li, Zhen-Hua, et al. "σ-aromaticity and σ-antiaromaticity in saturated inorganic rings." The Journal of Physical Chemistry A 109.16 (2005): 3711-3716.</ref>

Jw4116 Y2 inorg-comp

2018-05-25T16:49:39Z

Jw4116:

=PART 1=

==BH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity
|-
|1
|A2''
|1163
|93
|out-of-plane bend
|-
|2, 3
|x2 E'
|1213
|14
|bend
|-
|4
|A1'
|2582
|0
|symmetric stretch
|-
|5, 6
|x2 E'
|2715
|126
|aymmetric stretch
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|500px]]

MO diagram source <ref>http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>

==NH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEf(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1

Analysisː The bond energy value calculated is in the rough ballpark for normal bond energies (b.t.w 200-500kJ.mol-1) however, as it is a dative bond formed from a Lewis acid/base pair it will be weaker (lower energy) than a traditional covalent bond in which an electron is donated by each atom. This logic correlates with the value calculated.

==BBr3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)LANL2DZ

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
</pre>

BBr3 [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

=PART 2=

==Benzene==

[[File: SummarytableBenzeneJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000199 0.000450 YES
RMS Force 0.000081 0.000300 YES
Maximum Displacement 0.000847 0.001800 YES
RMS Displacement 0.000299 0.001200 YES
</pre>

Benzene [[Media: JW BENZENE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BENZENE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Borazine==

[[File: SummarytableBorazineJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000086 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
</pre>

Borazine [[Media: JW BORAZINE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BORAZINE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Analysis==

{| class="wikitable"
|+
|-
! Charge Distribution
! Atom (Pauling E.N)ː Gaussian Value
! Explanation
|-
|[[File: Charge-borazineJW4116.PNG|200px]]
|N (3.04)ː -1.102

B (2.04)ː 0.747

H-N (2.20)ː 0.432/ H-B (2.20)ː -0.077
|As shown in the picture and from general intuition from the knowledge of relative electronegativites, the charge distribution in borazine is very uneven. This is due to different hetero atoms having a exposed positive charge from the nucleus, increasing their ability to attract electron density from those atoms with a looser hold on their electrons. Although there is an uneven distribution of charge within the molecule, due to the symmetric distribution in charge, the molecule remains neutral with no single molecular dipole moment (they cancel out). The uneven distribution also results in a more reactive aromatic species as charges can attract nucleo/electrophillic species increasing the probability of a reaction (Nː nucleophillic, Bː electrophillic). Also half the protons would be more acidic than the other half based on their affinity to negative charge.
|-
|[[File: Charge-benzene.PNG|200px]]
|C (2.55)ː -0.239

H-C (2.20)ː 0.239

|Due to the higher symmetry of the benzene molecule (lack of heteroatoms) the charge distribution is even between each atom (H and C). As shown in the picture, the amount of charge on each atom is determined by their relative electronegativity and ability to attract electron density from the covalent bond. The symmetrical and even distribution in charge results in a very stable aromatic compound; however, the increased negative charge around the carbon atoms increases its imperceptibility to attack from strong electrophiles (seen in experiments).
|-
|}

==Comparing MOs==

{| class="wikitable"
|+
|-
! Benzene MO (no.)
! Borazine MO (no.)
! Comparison
|-
|[[File: MO14benzenejw4116.jpg|200px]]
|[[File: MO15borazinejw4116.jpg|200px]]
|These MOs are very similar in shape and nodal/ phase distribution. Due to the relative electronegativity, there is a slight distortion of electron density towards the nitrogen. However, due to the σ-nature of the MO, the distortion is much less due to the effectiveness of the overlap and rigidity of the MO. The contributing p-orbitals all lie in the same plane, perpendicular to the principle axis.
|-
|[[File: MO17benzenejw4116.jpg|200px]]
|[[File: MO17borazinejw4116.jpg|200px]]
|As with MO14/15 the shapes of these MOs are very similar with the same nodal/ phase distribution and roughly the same shape. The difference in electronegativity and distribution of electron density is demonstrated by the reduction in symmetry from Benzene (D6h) to Borazine (D3h) as the electrons favour the N atom. This is a much more significant effect than the previous MO comparison due to the relative high diffusivity of π orbitals compared to σ.
|-
|[[File: MO19benzenejw4116.jpg|200px]]
|[[File: MO18borazinejw4116.jpg|200px]]
|These wacky looking orbitals are also very similar but, like the other examples, have varied symmetry due to the distortion in electron density from the polarized bonds in the heteroaromatic ring. The effects of being bonded to electronegative atoms is seen in the contributions from the H1s orbitals to the MO. The hydrogens bonded to the nitrogen contribute significantly lower to the overall structure relative to those bonded to the boron atoms.
|-
|}

==Aromaticity==

Aromaticity is a very important concept in chemistry which relates to cyclic molecules and electron delocalisation. Aromatic compounds tend to be much less reactive than their more saturated counterparts due to the inherent stability associated with even electron distribution and delocalisation. A pioneer in the field of aromaticity was Hückel who devised a system/set of rules which determines the aromatic nature of a vast number of molecules. The rules require the molecule to have: 4n+2 π-electrons, be planar and have a connected system of delocalised p-orbitals along the principle axis of the molecule (perpendicular to the plane of the molecule). The classic aromatic molecule is benzene and its aromatic nature was first considered when the enthalpy of hydrogenation of poly-saturated cyclic hydrocarbons was studied; this confirmed that benzene was far more stable than expected which lead to the introduction of aromatic theory which was backed up by IR analysis. The effect of delocalisation and resulting ring current is seen in 1HNMR due to the induced magnetic field generated by the electrons whizzing around the pi system.

Nowadays, due to our more advanced analytical techniques, we have confirmed that a planar molecule with a system of delocalised electrons in a π MO is not a complete picture in describing the full extent/ nature and possible contributions leading to aromatic properties. One example would be the influence of σ-delocalised MOs (as seen in MO 14/15 above) which arises from the p-orbitals lying along the plane of the molecule. The electrons in this MO are clearly delocalised due to the nodal planes dissecting the nuclei rather than being inbetween them. The resulting MO is also lower in energy (more stable) than the π delocalised orbital due to the more effective σ overlap.<ref>Kovačević, Borislav, et al. "The origin of aromaticity: Important role of the sigma framework in benzene." ChemPhysChem 5.9 (2004): 1352-1364.</ref> Other examples of aromatic compounds that break Hückels rules exist which display delocalised electrons and aromatic properties such as saturated inorganic rings (SiH2)n and (GeH2)n and a variety of others molecules.<ref>Li, Zhen-Hua, et al. "σ-aromaticity and σ-antiaromaticity in saturated inorganic rings." The Journal of Physical Chemistry A 109.16 (2005): 3711-3716.</ref>

Jw4116 Y2 inorg-comp

2018-05-25T16:48:08Z

Jw4116:

=PART 1=

==BH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity

ǃMode
|-
|1
|A2''
|1163
|93
|out-of-plane bend
|-
|2, 3
|x2 E'
|1213
|14
|bend
|-
|4
|A1'
|2582
|0
|symmetric stretch
|-
|5, 6
|x2 E'
|2715
|126
|aymmetric stretch
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|500px]]

MO diagram source <ref>http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>

==NH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEf(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1

Analysisː The bond energy value calculated is in the rough ballpark for normal bond energies (b.t.w 200-500kJ.mol-1) however, as it is a dative bond formed from a Lewis acid/base pair it will be weaker (lower energy) than a traditional covalent bond in which an electron is donated by each atom. This logic correlates with the value calculated.

==BBr3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)LANL2DZ

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
</pre>

BBr3 [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

=PART 2=

==Benzene==

[[File: SummarytableBenzeneJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000199 0.000450 YES
RMS Force 0.000081 0.000300 YES
Maximum Displacement 0.000847 0.001800 YES
RMS Displacement 0.000299 0.001200 YES
</pre>

Benzene [[Media: JW BENZENE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BENZENE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Borazine==

[[File: SummarytableBorazineJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000086 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
</pre>

Borazine [[Media: JW BORAZINE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BORAZINE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Analysis==

{| class="wikitable"
|+
|-
! Charge Distribution
! Atom (Pauling E.N)ː Gaussian Value
! Explanation
|-
|[[File: Charge-borazineJW4116.PNG|200px]]
|N (3.04)ː -1.102

B (2.04)ː 0.747

H-N (2.20)ː 0.432/ H-B (2.20)ː -0.077
|As shown in the picture and from general intuition from the knowledge of relative electronegativites, the charge distribution in borazine is very uneven. This is due to different hetero atoms having a exposed positive charge from the nucleus, increasing their ability to attract electron density from those atoms with a looser hold on their electrons. Although there is an uneven distribution of charge within the molecule, due to the symmetric distribution in charge, the molecule remains neutral with no single molecular dipole moment (they cancel out). The uneven distribution also results in a more reactive aromatic species as charges can attract nucleo/electrophillic species increasing the probability of a reaction (Nː nucleophillic, Bː electrophillic). Also half the protons would be more acidic than the other half based on their affinity to negative charge.
|-
|[[File: Charge-benzene.PNG|200px]]
|C (2.55)ː -0.239

H-C (2.20)ː 0.239

|Due to the higher symmetry of the benzene molecule (lack of heteroatoms) the charge distribution is even between each atom (H and C). As shown in the picture, the amount of charge on each atom is determined by their relative electronegativity and ability to attract electron density from the covalent bond. The symmetrical and even distribution in charge results in a very stable aromatic compound; however, the increased negative charge around the carbon atoms increases its imperceptibility to attack from strong electrophiles (seen in experiments).
|-
|}

==Comparing MOs==

{| class="wikitable"
|+
|-
! Benzene MO (no.)
! Borazine MO (no.)
! Comparison
|-
|[[File: MO14benzenejw4116.jpg|200px]]
|[[File: MO15borazinejw4116.jpg|200px]]
|These MOs are very similar in shape and nodal/ phase distribution. Due to the relative electronegativity, there is a slight distortion of electron density towards the nitrogen. However, due to the σ-nature of the MO, the distortion is much less due to the effectiveness of the overlap and rigidity of the MO. The contributing p-orbitals all lie in the same plane, perpendicular to the principle axis.
|-
|[[File: MO17benzenejw4116.jpg|200px]]
|[[File: MO17borazinejw4116.jpg|200px]]
|As with MO14/15 the shapes of these MOs are very similar with the same nodal/ phase distribution and roughly the same shape. The difference in electronegativity and distribution of electron density is demonstrated by the reduction in symmetry from Benzene (D6h) to Borazine (D3h) as the electrons favour the N atom. This is a much more significant effect than the previous MO comparison due to the relative high diffusivity of π orbitals compared to σ.
|-
|[[File: MO19benzenejw4116.jpg|200px]]
|[[File: MO18borazinejw4116.jpg|200px]]
|These wacky looking orbitals are also very similar but, like the other examples, have varied symmetry due to the distortion in electron density from the polarized bonds in the heteroaromatic ring. The effects of being bonded to electronegative atoms is seen in the contributions from the H1s orbitals to the MO. The hydrogens bonded to the nitrogen contribute significantly lower to the overall structure relative to those bonded to the boron atoms.
|-
|}

==Aromaticity==

Aromaticity is a very important concept in chemistry which relates to cyclic molecules and electron delocalisation. Aromatic compounds tend to be much less reactive than their more saturated counterparts due to the inherent stability associated with even electron distribution and delocalisation. A pioneer in the field of aromaticity was Hückel who devised a system/set of rules which determines the aromatic nature of a vast number of molecules. The rules require the molecule to have: 4n+2 π-electrons, be planar and have a connected system of delocalised p-orbitals along the principle axis of the molecule (perpendicular to the plane of the molecule). The classic aromatic molecule is benzene and its aromatic nature was first considered when the enthalpy of hydrogenation of poly-saturated cyclic hydrocarbons was studied; this confirmed that benzene was far more stable than expected which lead to the introduction of aromatic theory which was backed up by IR analysis. The effect of delocalisation and resulting ring current is seen in 1HNMR due to the induced magnetic field generated by the electrons whizzing around the pi system.

Nowadays, due to our more advanced analytical techniques, we have confirmed that a planar molecule with a system of delocalised electrons in a π MO is not a complete picture in describing the full extent/ nature and possible contributions leading to aromatic properties. One example would be the influence of σ-delocalised MOs (as seen in MO 14/15 above) which arises from the p-orbitals lying along the plane of the molecule. The electrons in this MO are clearly delocalised due to the nodal planes dissecting the nuclei rather than being inbetween them. The resulting MO is also lower in energy (more stable) than the π delocalised orbital due to the more effective σ overlap.<ref>Kovačević, Borislav, et al. "The origin of aromaticity: Important role of the sigma framework in benzene." ChemPhysChem 5.9 (2004): 1352-1364.</ref> Other examples of aromatic compounds that break Hückels rules exist which display delocalised electrons and aromatic properties such as saturated inorganic rings (SiH2)n and (GeH2)n and a variety of others molecules.<ref>Li, Zhen-Hua, et al. "σ-aromaticity and σ-antiaromaticity in saturated inorganic rings." The Journal of Physical Chemistry A 109.16 (2005): 3711-3716.</ref>

Jw4116 Y2 inorg-comp

2018-05-25T16:46:34Z

Jw4116:

=PART 1=

==BH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity

ǃMode
|-
|1
|A2''
|1163
|93
|out-of-plane bend
|-
|2, 3
|x2 E'
|1213
|14
|bend
|-
|4
|A1'
|2582
|0
|symmetric stretch
|-
|5, 6
|x2 E'
|2715
|126
|aymmetric stretch
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|500px]]

==NH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEf(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1

Analysisː The bond energy value calculated is in the rough ballpark for normal bond energies (b.t.w 200-500kJ.mol-1) however, as it is a dative bond formed from a Lewis acid/base pair it will be weaker (lower energy) than a traditional covalent bond in which an electron is donated by each atom. This logic correlates with the value calculated.

==BBr3==

Calculation Method: RB3LYP

Basis Set: 6-31G(d,p)LANL2DZ

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
</pre>

BBr3 [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

=PART 2=

==Benzene==

[[File: SummarytableBenzeneJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000199 0.000450 YES
RMS Force 0.000081 0.000300 YES
Maximum Displacement 0.000847 0.001800 YES
RMS Displacement 0.000299 0.001200 YES
</pre>

Benzene [[Media: JW BENZENE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BENZENE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Borazine==

[[File: SummarytableBorazineJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000086 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
</pre>

Borazine [[Media: JW BORAZINE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BORAZINE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Analysis==

{| class="wikitable"
|+
|-
! Charge Distribution
! Atom (Pauling E.N)ː Gaussian Value
! Explanation
|-
|[[File: Charge-borazineJW4116.PNG|200px]]
|N (3.04)ː -1.102

B (2.04)ː 0.747

H-N (2.20)ː 0.432/ H-B (2.20)ː -0.077
|As shown in the picture and from general intuition from the knowledge of relative electronegativites, the charge distribution in borazine is very uneven. This is due to different hetero atoms having a exposed positive charge from the nucleus, increasing their ability to attract electron density from those atoms with a looser hold on their electrons. Although there is an uneven distribution of charge within the molecule, due to the symmetric distribution in charge, the molecule remains neutral with no single molecular dipole moment (they cancel out). The uneven distribution also results in a more reactive aromatic species as charges can attract nucleo/electrophillic species increasing the probability of a reaction (Nː nucleophillic, Bː electrophillic). Also half the protons would be more acidic than the other half based on their affinity to negative charge.
|-
|[[File: Charge-benzene.PNG|200px]]
|C (2.55)ː -0.239

H-C (2.20)ː 0.239

|Due to the higher symmetry of the benzene molecule (lack of heteroatoms) the charge distribution is even between each atom (H and C). As shown in the picture, the amount of charge on each atom is determined by their relative electronegativity and ability to attract electron density from the covalent bond. The symmetrical and even distribution in charge results in a very stable aromatic compound; however, the increased negative charge around the carbon atoms increases its imperceptibility to attack from strong electrophiles (seen in experiments).
|-
|}

==Comparing MOs==

{| class="wikitable"
|+
|-
! Benzene MO (no.)
! Borazine MO (no.)
! Comparison
|-
|[[File: MO14benzenejw4116.jpg|200px]]
|[[File: MO15borazinejw4116.jpg|200px]]
|These MOs are very similar in shape and nodal/ phase distribution. Due to the relative electronegativity, there is a slight distortion of electron density towards the nitrogen. However, due to the σ-nature of the MO, the distortion is much less due to the effectiveness of the overlap and rigidity of the MO. The contributing p-orbitals all lie in the same plane, perpendicular to the principle axis.
|-
|[[File: MO17benzenejw4116.jpg|200px]]
|[[File: MO17borazinejw4116.jpg|200px]]
|As with MO14/15 the shapes of these MOs are very similar with the same nodal/ phase distribution and roughly the same shape. The difference in electronegativity and distribution of electron density is demonstrated by the reduction in symmetry from Benzene (D6h) to Borazine (D3h) as the electrons favour the N atom. This is a much more significant effect than the previous MO comparison due to the relative high diffusivity of π orbitals compared to σ.
|-
|[[File: MO19benzenejw4116.jpg|200px]]
|[[File: MO18borazinejw4116.jpg|200px]]
|These wacky looking orbitals are also very similar but, like the other examples, have varied symmetry due to the distortion in electron density from the polarized bonds in the heteroaromatic ring. The effects of being bonded to electronegative atoms is seen in the contributions from the H1s orbitals to the MO. The hydrogens bonded to the nitrogen contribute significantly lower to the overall structure relative to those bonded to the boron atoms.
|-
|}

==Aromaticity==

Aromaticity is a very important concept in chemistry which relates to cyclic molecules and electron delocalisation. Aromatic compounds tend to be much less reactive than their more saturated counterparts due to the inherent stability associated with even electron distribution and delocalisation. A pioneer in the field of aromaticity was Hückel who devised a system/set of rules which determines the aromatic nature of a vast number of molecules. The rules require the molecule to have: 4n+2 π-electrons, be planar and have a connected system of delocalised p-orbitals along the principle axis of the molecule (perpendicular to the plane of the molecule). The classic aromatic molecule is benzene and its aromatic nature was first considered when the enthalpy of hydrogenation of poly-saturated cyclic hydrocarbons was studied; this confirmed that benzene was far more stable than expected which lead to the introduction of aromatic theory which was backed up by IR analysis. The effect of delocalisation and resulting ring current is seen in 1HNMR due to the induced magnetic field generated by the electrons whizzing around the pi system.

Nowadays, due to our more advanced analytical techniques, we have confirmed that a planar molecule with a system of delocalised electrons in a π MO is not a complete picture in describing the full extent/ nature and possible contributions leading to aromatic properties. One example would be the influence of σ-delocalised MOs (as seen in MO 14/15 above) which arises from the p-orbitals lying along the plane of the molecule. The electrons in this MO are clearly delocalised due to the nodal planes dissecting the nuclei rather than being inbetween them. The resulting MO is also lower in energy (more stable) than the π delocalised orbital due to the more effective σ overlap.<ref>Kovačević, Borislav, et al. "The origin of aromaticity: Important role of the sigma framework in benzene." ChemPhysChem 5.9 (2004): 1352-1364.</ref> Other examples of aromatic compounds that break Hückels rules exist which display delocalised electrons and aromatic properties such as saturated inorganic rings (SiH2)n and (GeH2)n and a variety of others molecules.<ref>Li, Zhen-Hua, et al. "σ-aromaticity and σ-antiaromaticity in saturated inorganic rings." The Journal of Physical Chemistry A 109.16 (2005): 3711-3716.</ref>

Jw4116 Y2 inorg-comp

2018-05-25T16:40:59Z

Jw4116: /* Charge Analysis */

=PART 1=

==BH3==

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity
|-
|1
|A2''
|1163
|93
|-
|2, 3
|x2 E'
|1213
|14
|-
|4
|A1'
|2582
|0
|-
|5, 6
|x2 E'
|2715
|126
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|500px]]

==NH3==

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEf(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1

Analysisː The bond energy value calculated is in the rough ballpark for normal bond energies (b.t.w 200-500kJ.mol-1) however, as it is a dative bond formed from a Lewis acid/base pair it will be weaker (lower energy) than a traditional covalent bond in which an electron is donated by each atom. This logic correlates with the value calculated.

==BBr3==

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
</pre>

BBr3 B3LYP/6-31G(d,p)LANL2DZ [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

=PART 2=

==Benzene==

[[File: SummarytableBenzeneJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000199 0.000450 YES
RMS Force 0.000081 0.000300 YES
Maximum Displacement 0.000847 0.001800 YES
RMS Displacement 0.000299 0.001200 YES
</pre>

Benzene [[Media: JW BENZENE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BENZENE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Borazine==

[[File: SummarytableBorazineJw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000086 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
</pre>

Borazine [[Media: JW BORAZINE FREQ OPT.LOG|.LOG file]]

<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW BORAZINE FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Analysis==

{| class="wikitable"
|+
|-
! Charge Distribution
! Atom (Pauling E.N)ː Gaussian Value
! Explanation
|-
|[[File: Charge-borazineJW4116.PNG|200px]]
|N (3.04)ː -1.102

B (2.04)ː 0.747

H-N (2.20)ː 0.432/ H-B (2.20)ː -0.077
|As shown in the picture and from general intuition from the knowledge of relative electronegativites, the charge distribution in borazine is very uneven. This is due to different hetero atoms having a exposed positive charge from the nucleus, increasing their ability to attract electron density from those atoms with a looser hold on their electrons. Although there is an uneven distribution of charge within the molecule, due to the symmetric distribution in charge, the molecule remains neutral with no single molecular dipole moment (they cancel out). The uneven distribution also results in a more reactive aromatic species as charges can attract nucleo/electrophillic species increasing the probability of a reaction (Nː nucleophillic, Bː electrophillic). Also half the protons would be more acidic than the other half based on their affinity to negative charge.
|-
|[[File: Charge-benzene.PNG|200px]]
|C (2.55)ː -0.239

H-C (2.20)ː 0.239

|Due to the higher symmetry of the benzene molecule (lack of heteroatoms) the charge distribution is even between each atom (H and C). As shown in the picture, the amount of charge on each atom is determined by their relative electronegativity and ability to attract electron density from the covalent bond. The symmetrical and even distribution in charge results in a very stable aromatic compound; however, the increased negative charge around the carbon atoms increases its imperceptibility to attack from strong electrophiles (seen in experiments).
|-
|}

==Comparing MOs==

{| class="wikitable"
|+
|-
! Benzene MO (no.)
! Borazine MO (no.)
! Comparison
|-
|[[File: MO14benzenejw4116.jpg|200px]]
|[[File: MO15borazinejw4116.jpg|200px]]
|These MOs are very similar in shape and nodal/ phase distribution. Due to the relative electronegativity, there is a slight distortion of electron density towards the nitrogen. However, due to the σ-nature of the MO, the distortion is much less due to the effectiveness of the overlap and rigidity of the MO. The contributing p-orbitals all lie in the same plane, perpendicular to the principle axis.
|-
|[[File: MO17benzenejw4116.jpg|200px]]
|[[File: MO17borazinejw4116.jpg|200px]]
|As with MO14/15 the shapes of these MOs are very similar with the same nodal/ phase distribution and roughly the same shape. The difference in electronegativity and distribution of electron density is demonstrated by the reduction in symmetry from Benzene (D6h) to Borazine (D3h) as the electrons favour the N atom. This is a much more significant effect than the previous MO comparison due to the relative high diffusivity of π orbitals compared to σ.
|-
|[[File: MO19benzenejw4116.jpg|200px]]
|[[File: MO18borazinejw4116.jpg|200px]]
|These wacky looking orbitals are also very similar but, like the other examples, have varied symmetry due to the distortion in electron density from the polarized bonds in the heteroaromatic ring. The effects of being bonded to electronegative atoms is seen in the contributions from the H1s orbitals to the MO. The hydrogens bonded to the nitrogen contribute significantly lower to the overall structure relative to those bonded to the boron atoms.
|-
|}

==Aromaticity==

Aromaticity is a very important concept in chemistry which relates to cyclic molecules and electron delocalisation. Aromatic compounds tend to be much less reactive than their more saturated counterparts due to the inherent stability associated with even electron distribution and delocalisation. A pioneer in the field of aromaticity was Hückel who devised a system/set of rules which determines the aromatic nature of a vast number of molecules. The rules require the molecule to have: 4n+2 π-electrons, be planar and have a connected system of delocalised p-orbitals along the principle axis of the molecule (perpendicular to the plane of the molecule). The classic aromatic molecule is benzene and its aromatic nature was first considered when the enthalpy of hydrogenation of poly-saturated cyclic hydrocarbons was studied; this confirmed that benzene was far more stable than expected which lead to the introduction of aromatic theory which was backed up by IR analysis. The effect of delocalisation and resulting ring current is seen in 1HNMR due to the induced magnetic field generated by the electrons whizzing around the pi system.

Nowadays, due to our more advanced analytical techniques, we have confirmed that a planar molecule with a system of delocalised electrons in a π MO is not a complete picture in describing the full extent/ nature and possible contributions leading to aromatic properties. One example would be the influence of σ-delocalised MOs (as seen in MO 14/15 above) which arises from the p-orbitals lying along the plane of the molecule. The electrons in this MO are clearly delocalised due to the nodal planes dissecting the nuclei rather than being inbetween them. The resulting MO is also lower in energy (more stable) than the π delocalised orbital due to the more effective σ overlap.<ref>Kovačević, Borislav, et al. "The origin of aromaticity: Important role of the sigma framework in benzene." ChemPhysChem 5.9 (2004): 1352-1364.</ref> Other examples of aromatic compounds that break Hückels rules exist which display delocalised electrons and aromatic properties such as saturated inorganic rings (SiH2)n and (GeH2)n and a variety of others molecules.<ref>Li, Zhen-Hua, et al. "σ-aromaticity and σ-antiaromaticity in saturated inorganic rings." The Journal of Physical Chemistry A 109.16 (2005): 3711-3716.</ref>

File:MO18borazinejw4116.jpg

2018-05-25T15:24:52Z

Jw4116:

File:MO19benzenejw4116.jpg

2018-05-25T15:24:05Z

Jw4116:

File:MO17borazinejw4116.jpg

2018-05-25T15:23:09Z

Jw4116:

File:MO17benzenejw4116.jpg

2018-05-25T15:22:19Z

Jw4116:

File:MO15borazinejw4116.jpg

2018-05-25T15:20:58Z

Jw4116:

File:MO14benzenejw4116.jpg

2018-05-25T15:20:11Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-25T14:24:20Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:23:57Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:23:23Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:21:24Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:21:07Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:20:50Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:19:48Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-25T14:19:17Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:18:27Z

Jw4116: /* Charge Analysis */

Jw4116 Y2 inorg-comp

2018-05-25T14:16:49Z

Jw4116:

File:Charge-benzene.PNG

2018-05-25T14:06:18Z

Jw4116:

File:Charge-borazineJW4116.PNG

2018-05-25T13:54:30Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T16:27:18Z

Jw4116:

File:JW BORAZINE FREQ OPT.LOG

2018-05-24T16:26:39Z

Jw4116:

File:SummarytableBorazineJw4116.PNG

2018-05-24T16:25:18Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T16:22:31Z

Jw4116:

File:JW BENZENE FREQ OPT.LOG

2018-05-24T16:21:47Z

Jw4116:

File:SummarytableBenzeneJw4116.PNG

2018-05-24T16:18:25Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T15:02:23Z

Jw4116:

==BH3==

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity
|-
|1
|A2''
|1163
|93
|-
|2, 3
|x2 E'
|1213
|14
|-
|4
|A1'
|2582
|0
|-
|5, 6
|x2 E'
|2715
|126
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|400px]]

==NH3==

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEf(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1

Analysisː The bond energy value calculated is in the rough ballpark for normal bond energies (b.t.w 200-500kJ.mol-1) however, as it is a dative bond formed from a Lewis acid/base pair it will be weaker (lower energy) than a traditional covalent bond in which an electron is donated by each atom. This logic correlates with the value calculated.

==BBr3==

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
</pre>

BBr3 B3LYP/6-31G(d,p)LANL2DZ [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

Jw4116 Y2 inorg-comp

2018-05-24T14:56:38Z

Jw4116:

==BH3==

[[File: BH3Summarytable.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES
</pre>

Frequency analysis log file [[Media:JUSTINWILSON BH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized BH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JUSTIN WILSON BH3 SYM FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[File: IRBH3SpectrumJW4116.PNG]]

{| class="wikitable"
|+
|-
! style="wikitable"| Mode

! Symmetry

! Frequency (± 100cm-1)

! Intensity
|-
|1
|A2''
|1163
|93
|-
|2, 3
|x2 E'
|1213
|14
|-
|4
|A1'
|2582
|0
|-
|5, 6
|x2 E'
|2715
|126
|-
|}

There are two reasons for the lack of 6 peaks in the IR spectrum, despite the number of modes calculated. The E' degenerate vibrational modes (2, 3 and 5, 6) absorb at the same frequency and hence cause the spectral peak to appear twice as large as the predicted intensity for 1 absorption. The other vibration (4) does not appears as it is IR inactive, symmetric and generates no dipole moment which is means it is unable to interact with the oscillating electric field.

[[File:BH3MOdiag.png|400px]]

==NH3==

[[File: JW4116SummarytableNH3.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000010 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

Frequency analysis log file [[Media:JW NH3 FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 1089.6618 1694.1735 1694.1738
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized NH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW NH3 FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3BNH3==

[[File: SummarytableH3NBH3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES
</pre>

Frequency analysis log file [[Media: NH3BH3 JW FREQ OPT.LOG|.LOG file]]

<pre>
Low frequencies --- 266.5949 632.3813 639.5072
</pre>

<jmol><jmolApplet>
<title> Frequency Optimized H3NBH3 </title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3BH3 JW FREQ OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==H3NBH3 Lewis Acid/Base B-N Bond Analysis==

E(BH3)ː -26.61532363 au

E(NH3)ː -56.55776863 au

E(H3NBH3)ː -83.22469007 au

ΔEf(H3NBH3)ː -0.05159781 au = -135.47 kJ.mol-1

==BBr3==

[[File: SummarytableBBr3Jw4116.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000015 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000066 0.001800 YES
RMS Displacement 0.000039 0.001200 YES
</pre>

BBr3 B3LYP/6-31G(d,p)LANL2DZ [[Media: JW4116-BBr3PseudoOPT.log|.LOG file]]

<jmol><jmolApplet>
<title>BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>JW4116-BBr3PseudoOPT.log</uploadedFileContents>
</jmolApplet></jmol>

File:NH3BH3 JW FREQ OPT.LOG

2018-05-24T14:55:42Z

Jw4116:

File:SummarytableH3NBH3Jw4116.PNG

2018-05-24T14:53:28Z

Jw4116:

File:JW NH3 FREQ OPT.LOG

2018-05-24T14:49:32Z

Jw4116:

File:JW4116SummarytableNH3.PNG

2018-05-24T14:47:07Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:38:29Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:38:01Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:37:37Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:31:59Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:30:46Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:30:19Z

Jw4116: /* BBr3 */

Jw4116 Y2 inorg-comp

2018-05-24T14:29:57Z

Jw4116:

File:SummarytableBBr3Jw4116.PNG

2018-05-24T14:29:44Z

Jw4116: Jw4116 uploaded a new version of File:SummarytableBBr3Jw4116.PNG

Jw4116 Y2 inorg-comp

2018-05-24T14:29:09Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T14:28:22Z

Jw4116:

File:JW4116-BBr3PseudoOPT.log

2018-05-24T14:27:11Z

Jw4116:

File:SummarytableBBr3Jw4116.PNG

2018-05-24T14:25:24Z

Jw4116:

Jw4116 Y2 inorg-comp

2018-05-24T13:37:47Z

Jw4116: