ChemWiki - User contributions [en]

Rep:Mod:EKJ1021

2014-10-23T22:13:45Z

Ej410: /* 3rd Year Computational Lab: Inorganic Module */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. BBr3 is a strong lewis acid with bromine withdrawing electron density from central boron atom. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

==== Chemical bond? ====

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease; frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

Because of their symmetries of D3h, both spectra show similar vibrations.

=== BH3 Molecular orbital diagram ===

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

=== Conclusion ===

By studying the electronic structure of benzene and its analogues boratabenzene, pyridine and borazine, it was seen that the orbitals appear significantly different depending on the nature of the atoms, for example electronegativity. Gaussian gave clear view and calculation of the constructed structures which helped to analyse the proposed structures.

Rep:Mod:EKJ1021

2014-10-23T22:06:54Z

Ej410: /* Aromaticity */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. BBr3 is a strong lewis acid with bromine withdrawing electron density from central boron atom. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

==== Chemical bond? ====

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease; frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

Because of their symmetries of D3h, both spectra show similar vibrations.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

=== Conclusion ===

By studying the electronic structure of benzene and its analogues boratabenzene, pyridine and borazine, it was seen that the orbitals appear significantly different depending on the nature of the atoms, for example electronegativity. Gaussian gave clear view and calculation of the constructed structures which helped to analyse the proposed structures.

Rep:Mod:EKJ1021

2014-10-23T21:50:48Z

Ej410: /* Vibrational spectrum for GaBr3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. BBr3 is a strong lewis acid with bromine withdrawing electron density from central boron atom. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

==== Chemical bond? ====

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease; frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

Because of their symmetries of D3h, both spectra show similar vibrations.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T21:49:25Z

Ej410: /* Vibrational spectrum for GaBr3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. BBr3 is a strong lewis acid with bromine withdrawing electron density from central boron atom. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

==== Chemical bond? ====

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease; frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

Because of their symmetries of D3h, both spectra show similar vibrations.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T21:45:35Z

Ej410: /* Geometry Analysis */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. BBr3 is a strong lewis acid with bromine withdrawing electron density from central boron atom. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

==== Chemical bond? ====

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T21:45:13Z

Ej410: /* Geometry Analysis */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. BBr3 is a strong lewis acid with bromine withdrawing electron density from central boron atom. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

==== Chemical bond? ====

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T14:14:03Z

Ej410: /* Vibrational spectrum for GaBr3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T14:12:30Z

Ej410: /* Vibrational spectrum for GaBr3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

The frequencies for GaBr3 are all significantly lower than those of BH3. The reason for this is because both central atom (B) and ligands (H) are substituted to atoms of higher masses. With increasing mass of the molecule, the vibrational frequency will decrease.

There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T14:08:05Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Because of the unsymmetrical nature and energy difference of boratabenzene, pyridine and borazine, the shape and energy of molecular orbitals of each will look different.

Rep:Mod:EKJ1021

2014-10-23T14:02:56Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! ChemDraw diagram
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T14:02:29Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| MO placement || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| MO placement || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| MO placement || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:56:51Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p orbital of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, giving overall highly bonding character.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approximately 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degree of symmetry depends on the nature of replaced units; thus pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:54:16Z

Ej410: /* Charge Distribution */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution was constructed from the NBO visualisations of Gaussian. The dark(red/blue) atoms show electonegative atoms and light(green) atoms give electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit in the place of C-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:52:47Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:52:28Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:52:10Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:51:38Z

Ej410: /* Boratabenzene */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one C-H unit substituted to B-H. Since B is less electonegative than C, charge distribution will appear differently. Also, the dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:50:16Z

Ej410: /* NBO analysis */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen; drawing electron towards itself. All charges add to zero giving overall zero charge. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:49:11Z

Ej410: /* Aromaticity */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other analogues of aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:42:47Z

Ej410: /* Vibrational spectrum for NH3BH3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:42:25Z

Ej410: /* BH3 Molecular orbital diagram */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

Molecular diagram was constructed with calculations from Gaussian and chemdraw. The energy levels are only estimated.

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:35:15Z

Ej410: /* Vibrational spectrum for NH3BH3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity ||IR active? ||type
|-
|266.2
|0
|no
|bend
|-
|632.1
|14
|no
|stretch
|-
|639.4
|4
|yes
|bend
|-
|639.5
|4
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1069
|41
|yes
|bend
|-
|1196
|109
|yes
|stretch
|-
|1204
|3
|yes
|bend
|-
|1204
|3
|yes
|bend
|-
|1329
|113
|yes
|stretch
|-
|1676
|28
|yes
|bend
|-
|1676
|28
|yes
|bend
|-
|2470
|67
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|2530
|230
|yes
|stretch
|-
|3462
|2
|no
|stretch
|-
|3579
|28
|yes
|stretch
|-
|3579
|28
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:33:17Z

Ej410: /* Vibrational spectrum for NH3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1090
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|-
|3589
|0.27
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:31:58Z

Ej410: /* Vibrational spectrum for BH3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || intensity || IR active? ||type
|-
|1163
|93
|yes
|bend
|-
|1213
|14
|very slight
|bend
|-
|1213
|14
|very slight
|bend
|-
|2583
|0
|no
|stretch
|-
|2716
|126
|yes
|stretch
|-
|2716
|126
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:19:48Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:19:31Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:19:18Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-

<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:19:01Z

Ej410: /* Frequency Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:17:53Z

Ej410: /* Frequency Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ FREQ.jpg]]
|-
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
-
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:17:17Z

Ej410: /* Vibrational spectrum for NH3BH3 */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|266.2
|no
|bend
|-
|632.1
|no
|stretch
|-
|639.4
|yes
|bend
|-
|639.5
|yes
|bend
|-
|1069
|yes
|bend
|-
|1069
|yes
|bend
|-
|1196
|yes
|stretch
|-
|1204
|yes
|bend
|-
|1204
|yes
|bend
|-
|1329
|yes
|stretch
|-
|1676
|yes
|bend
|-
|1676
|yes
|bend
|-
|2470
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|2530
|yes
|stretch
|-
|3462
|no
|stretch
|-
|3579
|yes
|stretch
|-
|3579
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ FREQ.jpg]]
|-

<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>

|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:16:20Z

Ej410: /* Optimisation */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-
|[[File:EKJ Benzene summary.jpg]]
|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ FREQ.jpg]]
|-

<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>

|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:16:03Z

Ej410: /* Frequency Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ FREQ.jpg]]
|-

<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>

|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:15:39Z

Ej410: /* Boratabenzene */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ FREQ.jpg]]
|-
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:15:24Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|-
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|-
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T13:15:05Z

Ej410: /* Borazine */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-
|[[File:EKJ borazine freq SUMM.jpg]]
|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T12:58:17Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms, showing overall highly bonding character
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Last MO diagrams are obviously p orbital pi overlap, this is possible because all C, N and B have p orbital available to interact. There are clear phase differences above and below the plane with no nodes so highly bonding character. Just like other comparison sets, the degrees of symmetry depend on the nature of replaced units; pyridine is highly unsymmetrical. Electrons are drawn towards nitrogen significantly on pyridine and borazine.

Rep:Mod:EKJ1021

2014-10-23T12:37:55Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

The second sets of MOs show p orbital sigma overlap between adjacent central atoms. For these, there are no contribution from H orbitals. Benzene and borazine are very highly symmetric with relatively low energy around -0.44 au. The MOs are unevenly distributed for boratabenzene and pyridine in the presence of one B-H unit and N-H consecutively; especially for pyridine, the orbitals are drawn towards electronegative N, highly distorted structure gives more negative energy compared to other analogues.

Rep:Mod:EKJ1021

2014-10-23T12:15:32Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine !! Overlap
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]] || [[File:EKJ 1.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976 || -
|-
| Level || 12 || 12 || 12 || 10 || -
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]] || [[File:EKJ 2.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622 || -
|-
| Level || 14 || 13 || 13 || 13 || -
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]] || [[File:EKJ 3.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795 || -
|-
| Level || 17 || 17 || 17 || 17 || -
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

File:EKJ 3.jpg

2014-10-23T12:13:40Z

Ej410:

File:EKJ 2.jpg

2014-10-23T12:13:20Z

Ej410:

File:EKJ 1.jpg

2014-10-23T12:13:00Z

Ej410:

Rep:Mod:EKJ1021

2014-10-23T12:08:03Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]]
|-
| Energy (au) || -0.5158 || -0.51429 || -0.77223 || -0.53976
|-
| Level || 12 || 12 || 12 || 10
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622
|-
| Level || 14 || 13 || 13 || 13
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795
|-
| Level || 17 || 17 || 17 || 17
|}

The first comparisons show overlap between s orbital of hydrogen and p of carbon, boron and nitrogen. As seen there is a phase difference between hydrogen and central atoms.
Benzene has a perfect symmetry whereas boratabenzene has a slightly distorted distribution due to a small difference in electronegativity between B and C(approx. 0.5). Similar energy of benzene and boratabenzene back up this idea.
However pyridine and borazine appear very differently. Nitrogen is significantly more electronegative than boron and carbon, so the presence of N polarise the molecule towards N itself. The pyridine MO show that electrons are drawn towards nitrogen. Also, for borazine where there are alternating B-H and N-H units, distribution is highly polarised towards nitrogen. It is more dynamic than pyridine because of the difference in electronegativity between N and B.
The highly unsymmetric distribution of pyridine results in more negative energy.

Rep:Mod:EKJ1021

2014-10-23T11:54:09Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ Comparison of MOs between benzene and benzene analogues
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]]
|-
| Energy (au) || -0.5158) || -0.51429 || -0.77223 || -0.53976
|-
| Level || 12 || 12 || 12 || 10
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622
|-
| Level || 14 || 13 || 13 || 13
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795
|-
| Level || 17 || 17 || 17 || 17
|}

Rep:Mod:EKJ1021

2014-10-23T11:53:26Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ caption
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]]
|-
| Energy (au) || -0.5158) || -0.51429 || -0.77223 || -0.53976
|-
| Level || 12 || 12 || 12 || 10
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]]
|-
| Energy (au) || -0.43943 || -0.42674 || -0.70196 || -0.43622
|-
| Level || 14 || 13 || 13 || 13
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]]
|-
| Energy (au) || -0.36088 || -0.34654 || -0.62501 || -0.36795
|-
| Level || 17 || 17 || 17 || 17
|}

Rep:Mod:EKJ1021

2014-10-23T11:45:49Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ caption
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]]
|-
| Level (Energy) || 12 (-0.51587) || 12 (-0.51429) || 12 (-0.77223) || 10 (-0.53976)
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]]
|-
| Level (Energy) || 14 (-0.43943) || 13 (-0.42674) || 13 (-0.70196) || 13 (-0.43622)
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]]
|-
| Level (Energy) || 17 (-0.36088) || 17 (-0.34654) || 17 (-0.62501) || 17 (-0.36795)
|}

Rep:Mod:EKJ1021

2014-10-23T11:43:24Z

Ej410: /* MO Comparison */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ caption
! Comparison !! Benzene !! Boratabenzene !! Pyridine !! Borazine
|-
| 1 || [[File:Benzene 2(12) -0.51587.jpg]] || [[File:Boratabenezene2(12) -0.51429.jpg]] || [[File:Pyridine2(12) -0.77223.jpg]] || [[File:Borazine2(10) -0.53976.jpg]]
|-
| 1 || energy level 12, -0.51587 || energy level 12, -0.51429 || energy level 12, -0.77223 || energy level 10, -0.53976
|-
| 2 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]]
|-
| 2 || energy level 14, -0.43943 || energy level 13, -0.42674 || energy level 13, -0.70196 || energy level 13, -0.43622
|-
| 3 || [[File:Benzene 3(17) -0.36088.jpg]] || [[File:Boratabenzene3(17) -0.34654.jpg]] || [[File:Pyridine3(17) -0.62501.jpg]] || [[File:Borazine3(17) -0.36795.jpg]]
|-
| 3 || energy level 17, -0.36088 || energy level 17, -0.34654 || energy level 17, -0.62501 || energy level 17, -0.36795
|}

Rep:Mod:EKJ1021

2014-10-23T11:38:09Z

Ej410: /* Aromaticity */

== 3rd Year Computational Lab: Inorganic Module ==

=== Constructing BH3 molecule ===

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 1) Result summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000655 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: B3LYP

Basis set: 3-21G

Calculation type: Optimisation(OPT)

The basis set of 3-21G determines the accuracy which is low in this case.

All three bond angles appeared to be 120 degrees.

{| class="wikitable" border="1"
|+ Bond distance (2.d.p)
! !! 2H !! 3H !! 4H
|-
| 1B || 1.53 || 1.54 || 1.55
|}

==== Convergence of BH3 molecule ====

[[File:EKJ(day 1) convergence.jpg]]

==== Total energy and RMS plot ====

[[File:EKJ(day 1) energy and gradient.jpg]]

We optimized the molecule to find the equilibrium point where there are no net forces on the molecule (The lowest point on the potential energy vs radius plot).

The 'Total Energy curve' gives information about the program traveling across potential energy surface(PES), whereas second plot gives 'Root Mean Square(RMS)' showing the gradient reaching zero as molecule approaches equilibrium point; minimum.

=== Optimisation ===

==== Improved basis sets ====

3-21G BH3 molecule is optimised to higher level basis set: 6-31G(d,p)

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) 631g summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000680 0.001800 YES
RMS Displacement 0.000412 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised ammonia molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ CH3 opt 631g part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Method: RB3LYP

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

Calculation type: Frequency

==== Molecule of BBr3 ====

Optimisation log file [[Media:Nh3_optimisation.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ(day 2) GaBr3 summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000000 0.000450 YES
RMS Force 0.000000 0.000300 YES
Maximum Displacement 0.000003 0.001800 YES
RMS Displacement 0.000002 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BBr3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ GaBr3 opt part2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Geometry Analysis ===

{| class="wikitable"
|+ geometry data
! !! BH3 !! BBr3 !! GaBr3
|-
| r(E-X) Å || 1.18 || 2.02 || 2.33
|-
| θ(X-E-X) degrees(º) || 120.00 || 120.00 || 120.00
|}

All molecules have bond angles of 120º expected from D3H molecule. However the bond lengths were different depending on the nature of central atom or the ligands due to several factors.

As ligands are substituted from BH3 to BBr3 significant change in bond length (0.84 Å) was observed because of the differences in size and bond strength of hydrogen and bromine. Bromine has many more electrons than hydrogen, and the outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen. Moreover since Br has 'partially filled 4p orbital' available for back-donation into empty B 2p orbital, which is simply not possible with hydrogen. These factors combine to give B-Br bond length smaller than expected value.

To compare between BBr3 and GaBr3, the difference in bond length is 0.31 Å. The central atom has changed from B to Ga; both in group 13 but Ga in further down on the group. This means that electrons in Ga are occupied in more diffuse 4p orbitals and B electrons in less diffuse 2p orbitals.
Since valence electrons of Br are also occupied in 4p orbitals, the interation between 4p-4p of Ga-Br would be stronger than that of 2p-40 B-Br. This results in stronger bonding.

Chemical bond is the way that two or more substances are held together by attraction of atoms through transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' forces which bind the atoms in a molecule. This is done by transferring or sharing electrons between atoms and depends significantly on the electrostatic force between protons in nucleus and electrons in the orbit. Typical strong bonds are ionic, covalent and metallic bonding.

In contrast, weak bonds are 'intermolecular' forces between molecules with dissociation energy of 4-13 KJ/mol. This force of attraction bind a molecule to another. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

=== BH3 frequency file ===

BH3:EKJ BH3/6-31G(d,p)
Frequency file: [[Media:EKJ BH3 FREQ.LOG| here]]

optimisation file: {{DOI|10042/31160}}

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:Summary freq.jpg]]
|
<pre>
Low frequencies --- -11.7227 -11.7149 -6.6070 0.0005 0.00278 0.4278
Low frequencies --- 1162.9743 1213.1388 1213.1390
</pre>
|}

==== Vibrational spectrum for BH3 ====
{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1163
|yes
|bend
|-
|1213
|very slight
|bend
|-
|12 13
|very slight
|bend
|-
|2583
|no
|stretch
|-
|2716
|yes
|stretch
|-
|2716
|yes
|stretch
|}

|[[File:IR spec.jpg]]

The IR spectrum obtained from six values of frequencies only give three peaks at 1163, 1213 and 2716 cm-1. The vibrations at 1213cm-1 and 2716cm-1 are degenerate, each giving one peak. Also, vibration at 2583 cm-1 is 'symmetric', hence not shown in IR spectrum.

=== GaBr3 frequency file ===

GaBr3:EKJ GaBr3
Frequency file: [[Media:EKJ GABR3 FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:GaBr3 freq summ.jpg]]
|
<pre>
Low frequencies --- 0.0153 0.0216 0.0236 46.8957 46.9079 46.9079
Low frequencies --- 94.3453 94.3456 141.7064
</pre>
|}

==== Vibrational spectrum for GaBr3 ====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|94.35
|
|no
|bend
|-
|94.35
|
|no
|bend
|-
|141.7
|
|very slight
|bend
|-
|172.5
|
|no
|stretch
|-
|275.1
|
|yes
|stretch
|-
|275.1
|
|yes
|stretch
|}

|[[File:GaBr3 IR spec.jpg]]

QUESTIONS!

What does the large difference in the value of the frequencies for BH3 compared to GaBr3 indicate?
There been a reordering of modes! This can be seen particularly in relation to the A2" umbrella motion. Compare the relative frequency and intensity of the umbrella motion for the two molecules. Looking at the displacement vectors how has the nature of the vibration changed? Why?

The frequencies for GaBr3 is significantly lower than BH3, this is because both central atom and ligands are substituted to another atoms of greater mass; B to Ga and H to Br.

==== BH3 Molecular orbital diagram ====

|[[File:EKJ asdMO.jpg]]

=== NH3 optimisation ===

Optimisation log file [[Media:NH3 opt.mol| here]]

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3 opt summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000024 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000079 0.001800 YES
RMS Displacement 0.000053 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>NH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== NH3 frequency file ===

NH3:EKJ NH3
Frequency file: [[Media:NH3 OPT log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:NH3 fre summ.jpg]]
|
<pre>
Low frequencies --- -30.7178 -0.0013 0.0007 0.0010 20.2209 28.2838
Low frequencies --- 1089.5549 1694.1246 1694.1858
</pre>
|}

==== Vibrational spectrum for NH3 ====

{| class="wikitable"
|+
|-
|wavenumber || IR active? ||type
|-
|1090
|yes
|bend
|-
|1694
|slight
|bend
|-
|1694
|slight
|bend
|-
|3461
|no
|stretch
|-
|3589
|no
|stretch
|-
|3589
|no
|stretch
|}

|[[File:NH3 IR spec.jpg]]

=== NBO analysis of NH3 ===

|[[File:EKJ NH3 charge.jpg]]

=== NH3BH3 Analysis ===

{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:NH3BH3 opt.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ NH3BH3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

NH3BH33:EKJ NH3BH3
Frequency file: [[Media:EKJ NH3BH3 log.txt| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ NH3BH3 freq summary.jpg]]
|
<pre>
Low frequencies --- 0.0010 0.0011 0.0012 17.3560 17.7505 38.8436
Low frequencies --- 266.2320 632.1439 639.3754
</pre>
|}

==== Vibrational spectrum for NH3BH3 ====

{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|266.2
|
|no
|bend
|-
|632.1
|
|no
|stretch
|-
|639.4
|
|yes
|bend
|-
|639.5
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1069
|
|yes
|bend
|-
|1196
|
|yes
|stretch
|-
|1204
|
|yes
|bend
|-
|1204
|
|yes
|bend
|-
|1329
|
|yes
|stretch
|-
|1676
|
|yes
|bend
|-
|1676
|
|yes
|bend
|-
|2470
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|2530
|
|yes
|stretch
|-
|3462
|
|no
|stretch
|-
|3579
|
|yes
|stretch
|-
|3579
|
|yes
|stretch
|}

|[[File:NH3BH3 IR.jpg]]

=== Determination of bond energy ===

E(NH3) = -56.5577686 au

E(BH3) = -26.6153236 au

E(NH3 BH3) = -83.2246889 au

ΔE = E(NH3 BH3) - [E(NH3)+E(BH3)]

= (-83.2246889)-[(-56.5577686)+(-26.6153236)]

= -0.0515967 au

1 au = 2625.50 kJ/mol

ΔE = - 135.47 kJ/mol

== Aromaticity ==

=== Benzene ===

The fragments made of benzene and its derivatives are classified as 'aromatics' which has meanings associated the stability resulting from its resonance properties. The identical bond lengths of C-H single bonds and double bonds was lead to Kekule structure with ring structure of π orbitals overlap.

Other aromatic compounds for example boratabenzene, pyridine and borazine have similar property and structure to benzene with one or more atoms substituted to another are expected to have different chemical and physical properties. Furthermore, since the ring atom is changed, the molecular orbital(MO) will also be changed significantly.

The aim of this project is to analyze benzene and its derivative using computational chemistry program Gaussian.

==== Optimisation ====

Benzene was first constructed using 3-21G basis set, then optimised to more accurate 6-31G basis set. The table below shows successive optimisation of the benzene molecule.

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ Benzene summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000198 0.000450 YES
RMS Force 0.000082 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000305 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Frequency analysis ====

Benzene
Frequency file: [[Media:EKJ BENZENE 6-31G FREQ.LOG| here]]

{| class="wikitable"
|+
! summary data !! low modes
|-

|[[File:EKJ Benzene freq summary.jpg]]
|
<pre>
Low frequencies --- -0.0008 -0.0007 0.0003 55.9811 56.8433 59.3704
Low frequencies --- 421.8710 422.0833 626.3430
</pre>
|}

|[[File:IR spec.jpg]]

==== NBO analysis ====

|[[File:benzene.jpg]]

As expected, benzene is a symmetrical molecule with symmetrical charge distribition. The carbon atoms appear to have -0.085 charge and that of hydrogen is +0.085. The reason that carbon has negative value is because it is more electronegative than hydrogen. All charges add to zero. The dipole moment is very close to zero as expected form charges and distribution of charges.

Optimisation log file [[Media:EKJ BENZENE 6-31G NBO.LOG| here]]

{| class="wikitable"
|+
! summary data || Jmol
|-

|[[File:EKJ Benzene NBO summary.jpg]]

|
<jmol><jmolApplet>
<title>benzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ benzene 6-31G NBO.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Molecular Orbital Diagram ====

Molecular orbital diagram for benzene was constructed by NBO analysis of Gaussian.

|[[File:Benzene MO2.jpg]]

=== Optimisation Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Summary.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000028 0.000300 YES
Maximum Displacement 0.000600 0.001800 YES
RMS Displacement 0.000171 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene negcharge 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Boratabenzene is an aromatic compound with one carbon atom substituted to borane. Since borane is less electonegative than carbon, charge distribution will appear differently on the NBO diagram. The dipole moment appear to be very different to that of benzene.

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ pyridine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000065 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000837 0.001800 YES
RMS Displacement 0.000178 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine is an aromatic compound with one C-H substituted to N-H unit. N is more electronegative than both carbon and borane.

==== Borazine ====

Optimisation log file [[Media:EKJ BENZENE 6-31G.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:EKJ borazine.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000249 0.001800 YES
RMS Displacement 0.000077 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazine 6-31G.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

=== Frequency Comparison ===

==== Boratabenzene ====

Optimisation log file [[Media:EKJ BORATABENZENE NEGCHARGE 6-31G MOL.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ FREQ.jpg]]

|
<pre>
Low frequencies --- -713.9558 -237.3218 -217.3403 -0.0009 -0.0009 -0.0007
Low frequencies --- 19.2226 278.1106 326.3331
</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ boratabenzene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Pyridine ====

Optimisation log file [[Media:EKJ PYRIDINE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ PYR SUMM.jpg]]

|
<pre>
Low frequencies --- 0.0004 0.0006 0.0009 122.2863 123.1958 133.4392
Low frequencies --- 430.1227 433.5911 621.7804

</pre>
|
<jmol><jmolApplet>
<title>Pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ pyridine 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==== Borazine ====

Optimisation log file [[Media:EKJ BORAZENE 6-31G FREQ.LOG| here]]
{| class="wikitable"
|+
! summary data !! Low modes || Jmol
|-

|[[File:EKJ borazine freq SUMM.jpg]]

|
<pre>
Low frequencies --- -431.1695 -423.1899 -422.8154 -198.5182 -0.0006 -0.0003
Low frequencies --- 0.0009 46.1688 47.1150
</pre>
|
<jmol><jmolApplet>
<title>Borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>EKJ borazene 6-31G freq.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is an inorganic aromatic compound with NH and BH units alternating. This compound has isostructural and isoelectrical properties to benzene which is why borazine is called 'inorganic benzene'.

=== Charge Distribution ===

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by colour
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ.jpg]]

||[[File:EKJ NBO COLOUR.jpg]]

||[[File:EKJ borazine COLOUR.jpg]]
|}

{| class="wikitable"
|+
! colspan="3" |Charge Distribution by number
|-

|Boratabenzene || Pyridine || Borazine
|-
|[[File:EKJ CHARGE BORATAZ NUMBER.jpg]]

||[[File:EKJ NBO NUMB.jpg]]

||[[File:EKJ borazine NUMB.jpg]]
|}

The charge distribution is clearly shown from the NBO visualisations of Gaussian. The dark(red) atoms means electonegative atoms and light(green) atoms are electopositive atoms.

Compare to NBO visualisations of benzene, there are significant differences on boratabenzene, pyridine and borazine. The colour and charge are given on the table.

Looking at boratabenzene, because of insertion of B-H unit, the symmetrical distribution is broken. B has charge of 0.015 which is larger compare to those of ortho, meta and para carbons(-0.054, -0.109, -0.049). Charge on H also appear different; hydrogen bonded to B bearing charge of -0.073, this is very different to other H bearing positive charges. This is because H is more electronegative than B so B-H gives polar nature. All charge add to zero.

For pyridine, again the symmetrical charge distribution is broken dye to insertion of electronegative N-H unit shown by blue colour on the distribution by number view. The high electronegative nitrogen distort the distribution more than boratabenzene; it can be seen that all Hs have much larger charge than for boratabenzene(0.510, 0.292, 0.301, 0.294). All charge add to 1.

Lastly, 'inorganic benzene' borazine is a symmetric molecule with overall charge of zero as expected. N and B bear charges of 0.436 and 0.271 which are significantly larger than values for boratabenzene and pyridine. H attached to N gives value 0.251 again much larger than -0.085 of B-H. The large difference in electronegativity between N and B increase overall polarity of the molecule.

=== MO Comparison ===

{| class="wikitable" border="1"
|+ caption
! MO !! Benzene !! Boratabenzene !! Pyridine !! Borazine
|-
| 1 || [[File:Benzene 1(14) -0.43943.jpg]] || [[File:Boratabenzene1(13) -0.42674.jpg]] || [[File:Pyridine1(13) -0.70196.jpg]] || [[File:Borazine1(13) -0.43622.jpg]]
|-
| cell || cell
|}

File:Pyridine3(17) -0.62501.jpg

2014-10-23T11:31:03Z

Ej410:

File:Pyridine2(12) -0.77223.jpg

2014-10-23T11:30:45Z

Ej410:

File:Pyridine1(13) -0.70196.jpg

2014-10-23T11:30:31Z

Ej410: