ChemWiki - User contributions [en]

Rep:Mod:soocho12

2014-12-19T11:46:09Z

Smc112: /* MO Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atoms and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron density towards itself. Bromine's outermost electron is occupied in 4p orbital which is much more diffuse and larger than 1s orbital of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atoms. Ga is much heavier atom than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallic bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lengh exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76
|3
|no
|bend
|-
|76
|3
|no
|bend
|-
|100
|9
|slight
|bend
|-
|197
|0
|no
|stretch
|-
|316
|57
|yes
|stretch
|-
|316
|57
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u

E(BH3)=-26.46226371 a.u

E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol

ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene. Therefore the dipole moment is similar to benzene; close to zero.

===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO shows this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pulls the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show high bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as it pulls electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they have different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:41:33Z

Smc112: /* Borazine:B3LYP/6-31G(d,p)level */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atoms and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron density towards itself. Bromine's outermost electron is occupied in 4p orbital which is much more diffuse and larger than 1s orbital of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atoms. Ga is much heavier atom than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallic bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lengh exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76
|3
|no
|bend
|-
|76
|3
|no
|bend
|-
|100
|9
|slight
|bend
|-
|197
|0
|no
|stretch
|-
|316
|57
|yes
|stretch
|-
|316
|57
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u

E(BH3)=-26.46226371 a.u

E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol

ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene. Therefore the dipole moment is similar to benzene; close to zero.

===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:39:18Z

Smc112: /* Determination of Bond Energy */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atoms and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron density towards itself. Bromine's outermost electron is occupied in 4p orbital which is much more diffuse and larger than 1s orbital of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atoms. Ga is much heavier atom than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallic bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lengh exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76
|3
|no
|bend
|-
|76
|3
|no
|bend
|-
|100
|9
|slight
|bend
|-
|197
|0
|no
|stretch
|-
|316
|57
|yes
|stretch
|-
|316
|57
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u

E(BH3)=-26.46226371 a.u

E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol

ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:38:11Z

Smc112: /* Geometry Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atoms and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron density towards itself. Bromine's outermost electron is occupied in 4p orbital which is much more diffuse and larger than 1s orbital of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atoms. Ga is much heavier atom than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallic bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together. This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lengh exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76
|3
|no
|bend
|-
|76
|3
|no
|bend
|-
|100
|9
|slight
|bend
|-
|197
|0
|no
|stretch
|-
|316
|57
|yes
|stretch
|-
|316
|57
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:33:37Z

Smc112: /* Vibrational spectrum for NH3 */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76
|3
|no
|bend
|-
|76
|3
|no
|bend
|-
|100
|9
|slight
|bend
|-
|197
|0
|no
|stretch
|-
|316
|57
|yes
|stretch
|-
|316
|57
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089
|145.4
|yes
|bend
|-
|1694
|13.6
|slight
|bend
|-
|1694
|13.6
|slight
|bend
|-
|3461
|1.1
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|-
|3590
|0.3
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:31:21Z

Smc112: /* Vibrational spectrum for GaBr3 */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76
|3
|no
|bend
|-
|76
|3
|no
|bend
|-
|100
|9
|slight
|bend
|-
|197
|0
|no
|stretch
|-
|316
|57
|yes
|stretch
|-
|316
|57
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:30:18Z

Smc112: /* Vibrational spectrum for BH3 */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</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:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:29:10Z

Smc112: /* Geometry Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.90 || 30.00 || 119.99
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:26:56Z

Smc112: /* Geometry Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting in stronger bonding.

Chemical bond is an attraction between atoms allowing the formation of chemical molecule by transferring and sharing electrons as well as electrostatic forces.

Strong bonds are 'intramolecular' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:24:29Z

Smc112: /* NBO analysis */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
Optimised file: [[Media:SC BENZENE NBO.LOG| here]]

[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

File:SC BENZENE NBO.LOG

2014-12-19T11:22:58Z

Smc112: Smc112 uploaded a new version of "File:SC BENZENE NBO.LOG"

Rep:Mod:soocho12

2014-12-19T11:22:31Z

Smc112: /* NBO Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom. This makes the adjacent carbon atoms electronegative; withdrawing electrons towards itself. Therefore the charge distribution is unsymmetrical. The dipole moment is 1.7338 due to the presence of electropositive boron atom.
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

The Nitrogen atom has the charge of -0.597 indicating that nitrogen is electronegative atom; withdrawing electrons towards itself. The presence of Nitrogen distorts the structure of the molecule, therefore the charge distribution is unsymmetrical. The dipole moment is 1.9483 due to the presence of electronegative nitrogen atom.
====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

The B-H unit and N-H unit are alternating in Borazine molecule which makes the molecule symmetrical; all Nitrogen atoms have the same charges of -1.102 indicating that nitrogen is electronegative atom whereas all Boron atoms have the charge of +0.747. The dipole moment is close to zero due to symmetrical charge distribution.

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T11:08:14Z

Smc112: /* NBO Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
Optimised file: [[Media:SC BORATABENZENE.LOG| here]]

[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

The Boron atom has the charge of 0.450 indicating that Boron is electropositive atom
====Pyridine====
Optimised file: [[Media:SC PYRIDINE NBO.LOG| here]]

[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

====Borazine====
Optimised file: [[Media:SC BORAZINE NBOS.LOG| here]]

[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

File:SC BORATABENZENE.LOG

2014-12-19T11:01:26Z

Smc112: Smc112 uploaded a new version of "File:SC BORATABENZENE.LOG"

File:SC BORAZINE NBOS.LOG

2014-12-19T11:00:23Z

Smc112:

File:SC PYRIDINE NBO.LOG

2014-12-19T11:00:04Z

Smc112:

File:SC BENZENE NBO.LOG

2014-12-19T10:59:03Z

Smc112:

Rep:Mod:soocho12

2014-12-19T10:58:27Z

Smc112:

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===NBO Comparison===

====Boratabenzene====
[[File:Sc boratabenzen nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc boratabenzene nbo.JPG]]

====Pyridine====
[[File:Sc pyridine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc pyridine nbo.JPG]]

====Borazine====
[[File:Sc borazine nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:SC borazine nbo.JPG]]

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T10:53:15Z

Smc112: /* NBO analysis */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]

As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T10:52:20Z

Smc112: /* NBO analysis */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
[[File:Sc benzene nbos.JPG]]
[[File:Sc benzene nboo.JPG]]
[[File:Sc benzene nbo.JPG]]
As benzene is a symmetrical molecule, it has a symmetrical charge distribution. All carbon atoms have -0.239 charges whereas hydrogen atoms have +0.239 charge. Carbon atoms has negative charges as they are more electronegative than hydrogen atoms; pulling electron towards itself. All charges add up to zero to give overall zero charge. The dipole moment is very close nearly zero due to symmetrical charge distribution.

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

File:Sc borazine nbos.JPG

2014-12-19T10:43:56Z

Smc112:

File:SC borazine nbo.JPG

2014-12-19T10:43:35Z

Smc112:

File:Sc pyridine nbos.JPG

2014-12-19T10:41:56Z

Smc112:

File:Sc pyridine nbo.JPG

2014-12-19T10:41:36Z

Smc112:

File:Sc boratabenzen nbos.JPG

2014-12-19T10:40:10Z

Smc112:

File:Sc boratabenzene nbo.JPG

2014-12-19T10:39:48Z

Smc112:

File:Sc benzene nbos.JPG

2014-12-19T10:37:05Z

Smc112:

File:Sc benzene nboo.JPG

2014-12-19T10:35:39Z

Smc112:

Rep:Mod:soocho12

2014-12-19T10:35:22Z

Smc112:

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

====NBO analysis====
[[File:Sc benzene nbo.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

File:SC BENZENE NBOo.mol

2014-12-19T10:32:14Z

Smc112:

File:Sc benzene nbo.JPG

2014-12-19T10:31:32Z

Smc112:

Rep:Mod:soocho12

2014-12-19T10:23:53Z

Smc112: /* MO Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:Sc chemdraw 14.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc chemdraw 12.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc chemdraw 17.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

File:Sc chemdraw 17.JPG

2014-12-19T10:22:31Z

Smc112:

File:Sc chemdraw 14.JPG

2014-12-19T10:22:13Z

Smc112:

File:Sc chemdraw 12.JPG

2014-12-19T10:21:44Z

Smc112:

Rep:Mod:soocho12

2014-12-19T10:15:01Z

Smc112:

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
{{DOI|10042/161092}}
====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

{{DOI|10042/161233}}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T00:52:19Z

Smc112: /* Geometry Comparison */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

BH3 and GaBr3 have 30º bond angles which is not quite right for D3H molecule. This shows that the molecules have not optimised properly. BBr3 has bond angle of 120º expected from D3H molecule. The bond lengths of 3 molecules are different to each other as they have different central atom and the ligands.

BH3 and BBr3 have different bond lengths due to different size and electronegativity of ligands. Bromine is highly electronegative atom which pulls the electron desity towards itself. Bromine's outermost electron is occupied in 4p orbitals which is much more diffuse and larger than 1s of hydrogen, therefore it interacts more strongly with Boron atom. Also, as Br's 4p orbital is partially filled, it is available for back-donation into empty B 2p orbital which gives more interaction with Boron atom. This gives B-Br bond length smaller than expected value.

GaBr3 and BBr3 have different bond lengths due to different central atom. Ga is much heavier group than B with more electrons occupying in more diffuse 4p orbitals. Br also has valence electrons occupied in 4p orbitals and the interaction between 4p-4p of Ga-Br would be more stronger than that of 2p-4p B-Br due to orbital match, resulting 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' the chemical bonds within a molecule. The bond is made by transferring or sharing electrons between atoms and depends on the electrostatic force between protons in nucleus and electrons in the orbit. This includes ionic, covalent and metallinc bonding.

Weak bonds are 'intermolecular' forces which is an attraction and repulsion between molecules that hold molecules, ions, and atoms together This includes hydrogen bonding, dipole-dipole interactions or London dispersion.

When we first optimised the molecule, the bond is not shown because there is a pre-defined value and if the bond lenght exceeds this value (in inorganic view), it does not appear.

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T00:21:11Z

Smc112: /* GaBr33:B3LYP/6-31G(d,p) */

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

The frequencies for GaBr3 are all significantly lower than those of BH3 as both the central atoms and ligands are higher in mass than the atoms of BH3. As the mass of the molecule increases, the vibrational frequency decreases. The frequency is inversely proportional to the square root of reduced mass of atoms in the molecules.

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T00:16:09Z

Smc112:

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-19T00:14:13Z

Smc112:

===Constructing BH3 molecule===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Optimisation===
====BH3:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====GaBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 GaBr3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====BBr3:B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

{{DOI|10042/149817}}

===Geometry Comparison===

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

===Frequency Analysis===
====BH3:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

====GaBr33:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===BH3 Molecular orbital diagram===

[[File:SC BBH3 MO.JPG|150px]]

===NH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3 Analysis===
====Optimisation====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency====
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

====Determination of Bond Energy====

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-18T23:22:12Z

Smc112:

===BH3===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===BH3===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===GaBr3===
====B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===BBr3===
====B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==Geometry Comparison==

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

===BH3:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

[[File:SC BBH3 MO.JPG|300px]]

===GaBr33:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===NH3===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===NH3:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===NH3BH3:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

===Dissociation energy===

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

==Aromaticity==
All aromatic molecules were optimised using the full basis set 6-31G(d,p).

===Benzene===
====Optimisation====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

====Frequency Analysis====
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

====Benzene MO Diagram====

[[File:SC benzene modiagram.JPG]]

===Optimisation Comparison===
====Boratabenzne:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}
Boratabenzne contains one "B-H" replacing of "C-H". An extra charge needs to be added to be isoelectronic as B is more electropositive than C. Therefore the energy of the molecule is slightly higher than benzene and the dipole moment is different to that of benzene.

====pyridine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Pyridine contains one "N-H" replacing of "C-H". An extra charge needs to be removed to be isoelectronic as N is more electronegative than C. Therefore the energy of the molecule is slightly lower than benzene and the dipole moment is different to that of benzene.
====Borazine:B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

Borazine is aromatic compound with NH and BH units alternating. As it is symmetric molecule, it is isostructural and isoelectric to benzene.
===Frequency Comparison===
====Boratabenzene:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

====Pyridine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

====Borazine:B3LYP/6-31G(d,p)====
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===

{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

The first set of MOs show the overlaps of s orbitals of hydrogen atoms and p orbitals of carbon, boron and nitrogen atoms. The phase difference between hydrogen atoms and central atoms represents highly bonding character. The MO energies of benzene and boratabenzene are similar to each other as electronegativity of boron is similar to electronegaivity of carbon. However the MO energies of pyridine and borazine are much lower than benzene and boratabenzene due to highly electronegative Nitrogen. The pyridine MO show the nitrogen atom polarise the molecule towards itself therefore the shapes of the MO are slightly distorted. The Borazine MO show this more significantly due to more nitrogen atoms are present.

The second set of MOs show the sigma overlaps of p orbitals of central atoms. The MO energies of benzene and borazine are similar to each other as their structures are highly symmetric. The MOs of boratabenzene and pyridine are quite distorted due to presence of one B-H unit and N-H unit consecutively. The MO energy of pyridine is much more lower than the others due to the presence of electronegative N atom and this pull the electrons towards itself making the MO more distorted.

The last set of MOs show the pi overlaps of p orbitals of central atoms. The phase differences between above and below the plane with no nodes show highly bonding character. Just like other sets of MOs, pyridine has the lowest MO energy due to the presence the most electronegative N atom which gives distortion of the molecule as they pull electrons towards itself.

The full MO diagrams of boratabenzene, pyridine and borazine will look different to each other as they different substituents with different energies and electronegativities.

Rep:Mod:soocho12

2014-12-18T21:32:10Z

Smc112:

===BH3===
====B3LYP/3-21G level====
Optimisation log file [[Media:SC BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC bh3 opt.jpg]]

|
<pre>

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC bh3 opt.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===BH3===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BH3 OPT 631G DP.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC_BH3_OPT_631g_dp.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000070 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000356 0.001800 YES
RMS Displacement 0.000214 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC_BH3_OPT_631g_dp.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===GaBr3===
====B3LYP/LANL2DZ====
Optimisation log file [[Media:SC GaBr3 pp opt1.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC GaBr3 pp optimisation.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 BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC GaBr3 pp 1 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===BBr3===
====B3LYP/LANL2DZ====
Optimisation log file [[Media:SC BBr3 OPT 631G DP.log| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BBr3 OPT 631G DP.jpg]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000035 0.001800 YES
RMS Displacement 0.000029 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>BBr3 mixed pseudo-potential and basis set optimisation</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC BBr3 OPT 631G DP.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

==Geometry Comparison==

{| class="wikitable"
|+ geometry data
! !! BH3 !! GaBr3 !! BBr3
|-
| r(E-X) Å || 1.20 || 2.39 || 2.02
|-
| θ(X-E-X) degrees(º) || 29.901 || 30 || 119.987
|}

===BH3:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc bh3 frequency.jpg|300px]]
|
<pre>
Low frequencies --- -12.4035 -12.3969 -7.7522 -0.0008 0.0236 0.4043
Low frequencies --- 1162.9690 1213.1353 1213.1355
</pre>
|}

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1162.97
|92.5688
|yes
|bend
|-
|1213.14
|14.0547
|very slight
|bend
|-
|1213.14
|14.0542
|very slight
|bend
|-
|2582.60
|0
|no
|stretch
|-
|2715.74
|126.3313
|yes
|stretch
|-
|2715.74
|126.3253
|yes
|stretch
|}

|[[File:Sc IR spectrum bh3 frequency.jpg|300px]]

{{DOI|10042/155385}}

[[File:SC BBH3 MO.JPG|300px]]

===GaBr33:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC GABR3 FREQUENCY.LOG| here]]

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

|[[File:Sc gabr3 frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -1.4878 -0.0015 -0.0002 0.0096 0.6540 0.6540
Low frequencies --- 76.3920 76.3924 99.6767
</pre>
|}

====Vibrational spectrum for GaBr3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|76.39
|3.3451
|no
|bend
|-
|76.39
|3.3450
|no
|bend
|-
|99.68
|9.2166
|slight
|bend
|-
|197.33
|0
|no
|stretch
|-
|316.18
|57.0655
|yes
|stretch
|-
|316.18
|57.0669
|yes
|stretch
|}

[[File:SC gabr3 ir.JPG]]

===NH3===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC NH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3 opt.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>
|
<jmol><jmolApplet>
<title>optimised NH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3 opt1.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===NH3:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC NH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3 freq.JPG|300px]]
|
<pre>
Low frequencies --- -0.0139 -0.0031 -0.0009 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>
|}

====Vibrational spectrum for NH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|1089.38
|145.4273
|yes
|bend
|-
|1693.94
|13.5570
|slight
|bend
|-
|1693.94
|13.5571
|slight
|bend
|-
|3461.30
|1.0595
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|-
|3589.86
|0.2699
|no
|stretch
|}

[[File:Sc NH3 IR.JPG]]

[[File:Sc nh3 nbo.JPG]]

[[File:SC NH3 NBOO.JPG]]

===NH3BH3===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC NH3BH3 OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC NH3BH3 opt1.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000513 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised NH3BH3 molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>SC NH3BH3 opt2.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===NH3BH3:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC NH3BH3 FREQUENCY.LOG| here]]

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

|[[File:Sc NH3bh3 frequency1.JPG|300px]]
|
<pre>
Low frequencies --- -0.0011 -0.0004 0.0009 17.3039 18.1059 37.5201
Low frequencies --- 265.8630 632.2227 639.3730
</pre>
|}

====Vibrational spectrum for NH3BH3====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|265.86
|0
|no
|bend
|-
|632.22
|14.0296
|slight
|stretch
|-
|639.37
|3.5492
|no
|bend
|-
|639.45
|3.5493
|no
|bend
|-
|1069.35
|40.5084
|yes
|bend
|-
|1069.39
|40.5106
|yes
|bend
|-
|1196.51
|109.0442
|yes
|stretch
|-
|1203.78
|3.4965
|no
|bend
|-
|1203.81
|3.4978
|no
|bend
|-
|1329.38
|113.5364
|yes
|stretch
|-
|1676.24
|27.5506
|yes
|bend
|-
|1676.24
|27.5522
|yes
|bend
|-
|2470.37
|67.2128
|yes
|stretch
|-
|2530.29
|231.3323
|yes
|stretch
|-
|2530.31
|231.3222
|yes
|stretch
|-
|3462.65
|2.5089
|no
|stretch
|-
|3759.59
|27.9221
|yes
|stretch
|-
|3759.61
|27.9227
|yes
|stretch
|}

[[File:SC NH3BH3 IR.JPG]]

===Dissociation energy===

E(NH3)=-56.55776873 a.u
E(BH3)=-26.46226371 a.u
E(NH3BH3)=-83.22468893 a.u

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-83.22468898-(-56.5577687-26.46226371)
=-0.20465657 a.u

1 a.u=2625.50 kj/mol
ΔE=-537.3258245 kj/mol

===Benzene===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BENZENE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC benzene opts.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>optimised benzene molecule</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc benzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===benzene:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC BENZENE FREQUENCY.LOG| here]]

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

|[[File:SC benzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -13.7810 -12.9763 -11.9029 -0.0009 -0.0009 -0.0002
Low frequencies --- 414.0699 414.1914 620.9703
</pre>
|}

====Vibrational spectrum for benzene====
{| class="wikitable"
|+
|-
|wavenumber || Intensity || IR active? ||type
|-
|414.07
|0
|no
|bend
|-
|414.19
|0
|no
|bend
|-
|620.97
|0
|no
|bend
|-
|620.99
|0
|no
|stretch
|-
|693.20
|74.2469
|yes
|bend
|-
|718.29
|0
|no
|bend
|-
|864.24
|0
|no
|bend
|-
|864.27
|0
|no
|bend
|-
|973.74
|0
|no
|bend
|-
|973.81
|0
|no
|bend
|-
|1012.46
|0
|no
|bend
|-
|1017.87
|0
|no
|bend
|-
|1019.92
|0
|no
|bend
|-
|1066.39
|3.4013
|no
|bend
|-
|1066.45
|3.4005
|no
|bend
|-
|1179.26
|0
|no
|bend
|-
|1202.22
|0
|no
|bend
|-
|1202.23
|0
|no
|bend
|-
|1356.07
|0
|no
|bend
|-
|1380.24
|0
|no
|bend
|-
|1524.39
|6.6149
|no
|bend
|-
|1524.44
|6.6185
|no
|bend
|-
|1653.03
|0
|no
|bend
|-
|1653.14
|0
|no
|bend
|-
|3174.37
|0.0004
|no
|stretch
|-
|3183.88
|0.0001
|no
|stretch
|-
|3183.98
|0.0001
|no
|stretch
|-
|3199.54
|46.5648
|yes
|stretch
|-
|3199.65
|46.5377
|yes
|stretch
|-
|3210.18
|0.0003
|no
|stretch
|}

[[File:SC benzene ir.JPG]]

===Benzene MO Diagram===

[[File:SC benzene modiagram.JPG]]

===Boratabenzne===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORATABENZENE.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:SC BORATABENZENE opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000152 0.000450 YES
RMS Force 0.000043 0.000300 YES
Maximum Displacement 0.000704 0.001800 YES
RMS Displacement 0.000172 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised boratabenzene</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc boratabenzene optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===pyridine===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC PYRIDINE OPTIMISATION.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc pyridine opts.JPG]]

|
<pre>
Item Value Threshold Converged?
Maximum Force 0.000157 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000859 0.001800 YES
RMS Displacement 0.000210 0.001200 YES

</pre>
|
<jmol><jmolApplet>
<title>optimised pyridine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc pyridine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===Borazine===
====B3LYP/6-31G(d,p)level====
Optimisation log file [[Media:SC BORAZINE OPT.LOG| here]]
{| class="wikitable"
|+
! summary data !! convergence || Jmol
|-

|[[File:Sc borazine opts.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>optimised borazine</title>
<color>lightgrey</color>
<size>200</size>
<uploadedFileContents>Sc borazine optj.mol</uploadedFileContents>
</jmolApplet></jmol>
|}

===boratabenzene:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC BORATABENZENE FREQUENCY.LOG| here]]

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

|[[File:SC boratabenzene frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -7.2032 -0.0009 0.0003 0.0004 1.9815 3.1157
Low frequencies --- 245.4562 344.7212 500.5873

</pre>
|}

===Pyridine:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC PYRIDINE FREQUENCY.LOG| here]]

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

|[[File:Sc pyridine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -252.1317 -9.0082 -7.6210 -0.0008 -0.0007 0.0004
Low frequencies --- 3.6141 242.7426 437.0176
</pre>
|}

===borazine:B3LYP/6-31G(d,p)===
Frequency file: [[Media:SC BORAZINE FREQUENCY.LOG| here]]

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

|[[File:SC borazine frequencys.JPG|300px]]
|
<pre>
Low frequencies --- -3.9223 -0.0011 -0.0010 -0.0008 7.4410 9.4491
Low frequencies --- 289.5787 289.7159 404.3426
</pre>
|}

===MO Comparison===
====Comparison of MOs between benzene and benzene analogues====
{| class="wikitable"
|+
! !! Benzene || Boratabenzene || Pyridine || Borazine ||ChemDraw diagram
|-

|1.
|[[File:SC boratabenzene mo 12.JPG|150px]]
|[[File:Sc benzene mo 12.JPG|150px]]
|[[File:SC pyridine mo 12.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|[[File:SC borazine mo 10.JPG|150px]]
|-
|Energy(au)
| -0.51795
| -0.50648
| -0.55092
| -0.55132
| -
|-
|MO placement
|12
|12
|12
|10
| -
|-
|2.
|[[File:SC benzene mo 14.JPG|150px]]
|[[File:SC boratabenzene mo 15.JPG|150px]]
|[[File:SC pyridine mo 14.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.43854
| -0.42598
| -0.45916
| -0.43197
| -
|-
|MO placement
|14
|15
|14
|15
| -
|-
|3.
|[[File:SC benzene mo 17.JPG|150px]]
|[[File:SC boratabenzene mo 17.JPG|150px]]
|[[File:SC pyridine mo 17.JPG|150px]]
|[[File:Sc borazine mo 17.JPG|150px]]
|[[File:Sc borazine mo 15.JPG|150px]]
|-
|Energy(au)
| -0.35999
| -0.36130
| -0.39718
| -0.36129
| -
|-
|MO placement
|17
|17
|17
|17
| -
|}

File:Sc borazine mo 17.JPG

2014-12-18T21:00:48Z

Smc112:

File:SC pyridine mo 17.JPG

2014-12-18T21:00:24Z

Smc112:

File:SC boratabenzene mo 17.JPG

2014-12-18T21:00:04Z

Smc112:

File:SC benzene mo 17.JPG

2014-12-18T20:59:45Z

Smc112:

File:Sc borazine mo 15.JPG

2014-12-18T20:59:19Z

Smc112:

File:SC pyridine mo 14.JPG

2014-12-18T20:58:51Z

Smc112:

File:SC boratabenzene mo 15.JPG

2014-12-18T20:58:29Z

Smc112:

File:SC benzene mo 14.JPG

2014-12-18T20:58:05Z

Smc112: