ChemWiki - User contributions [en]

Rep:Mod:dianaberheci

2018-05-11T14:49:04Z

Db2716:

==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration <ref name="one" />. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure 4: Molecular Orbital Diagram for BH3 <ref name="two" />]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO <ref name="two" />]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO <ref name="two" />]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO <ref name="two" />]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO <ref name="two" />]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO <ref name="two" />]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO <ref name="two" />]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO <ref name="two" />]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 5: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 6: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol <ref name="three" /> (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> <ref name="three" />, which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 7: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure 8:IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure 9:Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure 10:Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure 11: Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure 12: Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. <ref name="four" /> Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure 13: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems. <ref name="five" />

==References==

<div style="text-align: justify;">
<references>

<ref name="one">J.M. Brown, Molecular Spectroscopy, Oxford University Press, 1998 </ref>

<ref name="two">Dr. P. Hunt, Molecular Orbitals in Inorganic Chemistry 2nd year UG course, Imperial College London, November, 2017 </ref>

<ref name="three">A. Haaland, Anxrw. Chem. Inl. Ed. Engl., 1989, 28, 992-1007 </ref>

<ref name="four">M. Sainsbury, Aromatic Chemistry, Oxford University Press, 1992 </ref>

<ref name="five">P. Atkins, J. de Paula, Atkins' Physical Chemistry, Oxford University Press, 2014, 894-902</ref>
</references>

Rep:Mod:dianaberheci

2018-05-11T14:37:55Z

Db2716: /* Aromaticity concepts */

==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration <ref name="one" />. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 <ref name="two" />]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO <ref name="two" />]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO <ref name="two" />]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO <ref name="two" />]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO <ref name="two" />]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO <ref name="two" />]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO <ref name="two" />]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO <ref name="two" />]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol <ref name="three" /> (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> <ref name="three" />, which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. <ref name="four" /> Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems. <ref name="five" />

Rep:Mod:dianaberheci

2018-05-11T14:36:54Z

Db2716: /* Association Energy */

==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration <ref name="one" />. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 <ref name="two" />]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO <ref name="two" />]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO <ref name="two" />]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO <ref name="two" />]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO <ref name="two" />]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO <ref name="two" />]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO <ref name="two" />]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO <ref name="two" />]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol <ref name="three" /> (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> <ref name="three" />, which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:35:58Z

Db2716: /* Molecular Orbitals analysis */

==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration <ref name="one" />. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 <ref name="two" />]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO <ref name="two" />]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO <ref name="two" />]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO <ref name="two" />]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO <ref name="two" />]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO <ref name="two" />]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO <ref name="two" />]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO <ref name="two" />]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:34:52Z

Db2716: /* Vibrations analysis */

==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration <ref name="one" />. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:34:06Z

Db2716: /* To do list */

==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:31:53Z

Db2716: /* Aromaticity concepts */

==To do list==


2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

{| class='wikitable'
|+
|[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]
|}

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:31:04Z

Db2716: /* BBr3 optimisation */

==To do list==


2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

Compared to BH3, BBr3 will show vibrations of much lower frequency, giving less peaks in the IR spectrum due to the small intensities of the respective vibrations. This is because bromine atoms are much heavier than hydrogen atoms, and the molecular weight of the molecule increases significantly, thus reducing the vibration frequencies.

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:28:16Z

Db2716: /* Molecular Orbitals Comparison */

==To do list==


2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] || In both molecules, this MO arises from combinations of 2s orbitals only, therefore they are sigma molecular orbitals. In benzene, although the MO has a nodal plane separating the 2 phases, it has an overall bonding character. Each hydrogen atom also contributes, and there are no out-of-phase s(C)-s(H) interactions, meaning there is a strong bonding character between the carbons and hydrogens. The borazine equivalent looks similar, however it won't have any contributions from the hydrogen atoms on borons. Also, 2 out of the 3 boron atoms in the molecule do not contribute to this MO. Overall, the borazine MO has less of a bonding character than the one in benzene.
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] || The 17th MO in benzene is the first valence MO of the molecule. It looks very similar to the MO obtained from the LCAO method, and it involves in-phase interactions between the pz atomic orbitals. The borazine equivalent exhibits the same characteristics and looks almost identical to the benzene MO.
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] || This is a weakly-bonding MO in benzene, as even if it has a nodal plane passing through 2 of the carbon atoms in the molecule, the other 2 pairs of pz orbitals interact favourably. The equivalent in borazine looks fairly similar and has a weakly bonding character as well, but the size of the MO is different around nitrogen and boron: nitrogen is more electronegative than boron, so it will attract the electrons more. Therefore, the nitrogen has a higher contribution to the MO than boron. In benzene, all atoms involved in the aromaticity are the same, meaning there are no different orbital contributions.
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

Rep:Mod:dianaberheci

2018-05-11T14:07:55Z

Db2716:

==To do list==


2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Usually, aromaticity is a concept applying to cyclic, planar, conjugated systems which obey Huckel's rule of 4n+2 pi electrons. This rule states that aromatic compounds must have 4n+2 pi delocalised electrons. Aromatic compounds are much more stable than equivalent compounds exhibiting localised double bonds and they do not usually undergo electrophilic additions to the double bonds; instead, they are subject to aromatic electrophilic substitutions.

In classic compounds, such as benzene, the origin of aromaticity is related to the overlap of the pz orbitals from each carbon involved in the conjugated system. For example, in benzene, each carbon atom is sp2 hybridised, which means each of the carbons has a pz orbital perpendicular to the ring plane. The 6 pz atomic orbitals will overlap, creating regions of delocalised electrons above and below the plane of the benzene ring.

A better picture of the aromaticity in benzene is given by the molecular orbitals of benzene (see Figure x). Thus, it can be seen that the lowest molecular orbital π1 has got the highest bonding character, while following 2 have a weaker bonding character. These 3 bonding molecular orbitals will all be completely filled, and the last 3 molecular orbitals, the anti-bonding ones, will be empty. This confers a very high stability to benzene, as it has got the maximal stabilisation it can achieve, as all its bonding molecular orbitals filled with electron pairs.

[[File: DbMobenzene.png|650px|thumb|Figure x: MO diagram for benzene]]

Apart from the ability of the π orbitals to accommodate all the electrons exclusively in the bonding orbitals, the σ-framework of the benzene (formed by the sp2 atomic orbitals of each carbon) contributes to the stability, as the σ bonds arrange in a hexagon shape, which allows for a perfect C-C-C bond angle of 120 degrees, therefore the σ framework does not suffer of any strain. These features add up to the stability of the aromatic systems.

File:DbMobenzene.png

2018-05-11T14:06:53Z

Db2716:

Rep:Mod:dianaberheci

2018-05-10T23:16:56Z

Db2716: /* Charge Distribution Comparison */

==To do list==


2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

In benzene, the ring is formed by six identical carbons, each connected to one hydrogen. Therefore, the molecule will not have a varied charge distribution. As carbon is slightly more electronegative than hydrogen, it will have a slightly higher electron density than hydrogen.
However, borazine, although having a zero dipole moment, shows a more complicated charge distribution. This arises as a consequence of the differences in electronegativities between nitrogen, hydrogen and boron (nitrogen is the most electronegative, followed by hydrogen and boron). Therefore, the N-H bonds will be polarised towards nitrogen (which will have a more negative charge), whereas the B-H bonds will be polarised towards hydrogen, leaving the borons to be more electron deficient.

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Ref: http://www.ch.ic.ac.uk/rzepa/spiro/

Rep:Mod:dianaberheci

2018-05-10T23:09:04Z

Db2716: /* To do list */

==To do list==


2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Ref: http://www.ch.ic.ac.uk/rzepa/spiro/

Rep:Mod:dianaberheci

2018-05-10T23:07:50Z

Db2716: /* Molecular Orbitals analysis */

==To do list==


1. MO analysis for BH3

2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding || The first MO of BH3 is very deep, therefore it won't be involved in bonding. The orbital is very close to the boron nucleus, as it is essentially arising from the 1s orbital of boron.
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] || The second MO of BH3 is a sigma orbital which has an overall bonding character. It is formed by the in phase combination of the 2s orbital of boron and the H3 orbital with a1' symmetry. Gaussian and LCAO method both give very similarly shaped MOs.
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] || The third MO arises from the sigma in-phase interaction between the 2py orbital of boron and one of the e' H3 orbitals. The MO is higher in energy than the previous one as it has got a nodal plane along the x axis. The 2 representations are again fairly similar, but it is important to note that Gaussian gives a more accurate picture of the MO, as it accounts for the final MO shape resulting from the combination of the FMOs: the resulting MO is more dense towards the hydrogen atoms and less dense towards the other hydrogen on the x axis.
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] || This MO arises from the in-phase interactions between the 2px of boron and the other e' of H3. There is a nodal plane along the z axis now. The 2 representations are fairly similar, but the Gaussian one is again more representative for the real situation, as it accounts for the in-phase interactions between the 2H and the green lobe of the p orbital.
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] || The fifth MO is the non-bonding MO of BH3, as the pz orbital does not have the right symmetry to interact with any of the H3 orbitals. Whilst both pictures are similar, the Gaussian image accounts for the large size of this orbital and the extension of its surface towards the B-H bonds.
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] || The sixth MO is the LUMO and it is formed from the out-of-phase interactions between the 2s of boron and the a1' symmetry orbital from H3, leading to an anti-bonding MO.
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] || The seventh MO looks slightly different in the 2 representations, as in the Gaussian model, the orbital electron density is extended towards the x axis as well. The interactions are again out-of-phase, leading to an anti-bonding orbital.
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] || This MO does not have the exact same shape as described by the LCAO, as the shapes of the orbitals making up the MO change upon forming the MO. This MO is composed of out-of-phase interactions, and it is an anti-bonding one.
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Ref: http://www.ch.ic.ac.uk/rzepa/spiro/

Rep:Mod:dianaberheci

2018-05-10T14:30:06Z

Db2716: /* Aromaticity concepts */

==To do list==


1. MO analysis for BH3

2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Ref: http://www.ch.ic.ac.uk/rzepa/spiro/

Rep:Mod:dianaberheci

2018-05-10T14:07:10Z

Db2716: /* To do list */

==To do list==


1. MO analysis for BH3

2. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:57:44Z

Db2716: /* Charge Distribution Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
| 0.239
|-
|Borazine
|Boron (all 3 borons identical)
| 0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
| 0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:57:26Z

Db2716: /* Charge Distribution Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
| -0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
|0.239
|-
|Borazine
|Boron (all 3 borons identical)
|0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
| -1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
| -0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
|0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:56:54Z

Db2716: /* Charge Distribution Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

{| class="wikitable"
|+ Charge distributions in benzene and borazine, tabulated
|-
|Molecule || Atom || Charge
|-
|Benzene
|Carbon (all 6 carbons identical)
|-0.239
|-
|Benzene
|Hydrogen (all 6 hydrogens identical)
|0.239
|-
|Borazine
|Boron (all 3 borons identical)
|0.747
|-
|Borazine
|Nitrogen (all 3 nitrogens identical)
|-1.102
|-
|Borazine
|Hydrogens connected to boron atoms (3 hydrogens)
|-0.077
|-
|Borazine
|Hydrogens connected to nitrogen atoms (3 hydrogens)
|0.432

|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:44:14Z

Db2716: /* Association Energy */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

The dissociation energy of the B-N covalent bond is 389 kJ/mol [r] (thus, -389 kJ/mol for association). However, the bond energy between B and N in NH3BH3 is about a third of the literature value, meaning that the bond strength between B and N in this compound is much weaker. This fits the theory model well, as the B-N bond here is not a simple covalent bond, it's a dative covalent bond formed by donation of a lone pair of electrons from nitrogen to an empty p orbital of boron.
Indeed, the literature value for a dative B-N bond is <math>\Delta E = -130.122 \pm 1 kJ/mol </math> [r], which is very close to the one obtained from the Gaussian calculations, thus confirming the nature of the B-N bond in NH3BH3.
The dative bond is rather weak compared to a simple covalent bond because upon heterolytic breaking, the bond yields 2 stable compounds, ammonia and borane.

Ref1: https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf

Ref2: Arne Haaland, Anxrw. Chem. Inl. Ed. Engl. 28 (1989) 992-1007

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:12:34Z

Db2716: /* Association Energy */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = -135.524 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:08:53Z

Db2716: /* Project: Aromaticity */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

===Aromaticity concepts===

Rep:Mod:dianaberheci

2018-05-10T13:01:59Z

Db2716: /* Charge Distribution Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|-
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

Rep:Mod:dianaberheci

2018-05-10T13:01:40Z

Db2716: /* Charge Distribution Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

{| class="wikitable"
|+
|[[File:Db benzene charges good.PNG|650px|thumb|Figure : Benzene charge distribution]]
|[[File:Db borazine chargesgood.PNG|650px|thumb|Figure : Borazine charge distribution]]
|}

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

File:Db borazine chargesgood.PNG

2018-05-10T13:01:26Z

Db2716:

File:Db benzene charges good.PNG

2018-05-10T12:57:45Z

Db2716:

Rep:Mod:dianaberheci

2018-05-10T12:54:49Z

Db2716: /* Molecular Orbitals Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|9th MO]] ||[[File:Db borazine mo9.png|left|300px|thumb|9th MO]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|17th MO ]] ||[[File:Db borazine mo17.png|left|300px|thumb|17th MO]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|20th MO]] ||[[File:Db borazine mo20.png|left|300px|thumb|20th MO]] ||
|}

Rep:Mod:dianaberheci

2018-05-10T12:53:07Z

Db2716: /* Molecular Orbitals Comparison */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:Db benzene mo9.png|left|300px|thumb|2nd MO from Gaussian]] ||[[File:Db borazine mo9.png|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:Db benzene mo17.png|left|300px|thumb|3rd MO from Gaussian]] ||[[File:Db borazine mo17.png|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:Db benzene mo20.png|left|300px|thumb|4th MO from Gaussian]] ||[[File:Db borazine mo20.png|left|200px|thumb|4th MO from LCAO [r]]] ||
|}

File:Db borazine mo20.png

2018-05-10T12:52:32Z

Db2716:

File:Db benzene mo20.png

2018-05-10T12:52:07Z

Db2716:

File:Db borazine mo17.png

2018-05-10T12:51:39Z

Db2716:

File:Db benzene mo17.png

2018-05-10T12:51:03Z

Db2716:

File:Db borazine mo9.png

2018-05-10T12:50:26Z

Db2716:

File:Db benzene mo9.png

2018-05-10T12:49:36Z

Db2716:

Rep:Mod:dianaberheci

2018-05-10T12:44:28Z

Db2716: /* Project: Aromaticity */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution Comparison===

===Molecular Orbitals Comparison===

{| class="wikitable" border="1"
|+ Comparison of benzene and borazine molecular orbitals
! scope="col" style="width: 275px;" | Benzene Molecular Orbital
! scope="col" style="width: 100px;" | Borazine Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

Rep:Mod:dianaberheci

2018-05-10T12:42:08Z

Db2716: /* Benzene analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| benzene]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:dianaberheci

2018-05-10T12:41:40Z

Db2716: /* Borazine analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| borazine]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:dianaberheci

2018-05-10T12:39:36Z

Db2716: /* Borazine analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| DB BORAZINE OPT2.LOG]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Borazine optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:dianaberheci

2018-05-10T12:01:30Z

Db2716: /* Project: Aromaticity */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| DB BORAZINE OPT2.LOG]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BORAZINE OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:dianaberheci

2018-05-10T11:59:55Z

Db2716: /* Borazine analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BORAZINE OPT2.LOG| DB BORAZINE OPT2.LOG]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

File:DB BORAZINE OPT2.LOG

2018-05-10T11:59:32Z

Db2716:

Rep:Mod:dianaberheci

2018-05-10T11:56:07Z

Db2716: /* Borazine analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -6.5952 -6.4169 -5.9633 -0.0097 0.0576 0.1409
Low frequencies --- 289.2513 289.2617 403.8549
</pre>

Rep:Mod:dianaberheci

2018-05-10T11:46:36Z

Db2716: /* Project: Aromaticity */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

{| class="wikitable"
|+
|[[File:Db borazine summary.PNG|650px|thumb|Figure :Summary table for optimised borazine]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

File:Db borazine summary.PNG

2018-05-10T11:44:54Z

Db2716:

Rep:Mod:dianaberheci

2018-05-10T11:43:38Z

Db2716: /* Borazine analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

<pre>
Item Value Threshold Converged?
Maximum Force 0.000085 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000251 0.001800 YES
RMS Displacement 0.000075 0.001200 YES
Predicted change in Energy=-9.309158D-08
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,9) 1.0098 -DE/DX = 0.0 !
! R2 R(2,11) 1.1949 -DE/DX = 0.0001 !
! R3 R(3,8) 1.0098 -DE/DX = 0.0 !
! R4 R(4,10) 1.1949 -DE/DX = 0.0001 !
! R5 R(5,7) 1.0098 -DE/DX = 0.0 !
! R6 R(6,12) 1.1949 -DE/DX = 0.0001 !
! R7 R(7,10) 1.4307 -DE/DX = -0.0001 !
! R8 R(7,12) 1.4307 -DE/DX = -0.0001 !
! R9 R(8,10) 1.4307 -DE/DX = -0.0001 !
! R10 R(8,11) 1.4307 -DE/DX = -0.0001 !
! R11 R(9,11) 1.4307 -DE/DX = -0.0001 !
! R12 R(9,12) 1.4307 -DE/DX = -0.0001 !
! A1 A(5,7,10) 118.5609 -DE/DX = 0.0 !
! A2 A(5,7,12) 118.5609 -DE/DX = 0.0 !
! A3 A(10,7,12) 122.8782 -DE/DX = 0.0 !
! A4 A(3,8,10) 118.5609 -DE/DX = 0.0 !
! A5 A(3,8,11) 118.5609 -DE/DX = 0.0 !
! A6 A(10,8,11) 122.8782 -DE/DX = 0.0 !
! A7 A(1,9,11) 118.5609 -DE/DX = 0.0 !
! A8 A(1,9,12) 118.5609 -DE/DX = 0.0 !
! A9 A(11,9,12) 122.8782 -DE/DX = 0.0 !
! A10 A(4,10,7) 121.4391 -DE/DX = 0.0 !
! A11 A(4,10,8) 121.4391 -DE/DX = 0.0 !
! A12 A(7,10,8) 117.1218 -DE/DX = 0.0 !
! A13 A(2,11,8) 121.4391 -DE/DX = 0.0 !
! A14 A(2,11,9) 121.4391 -DE/DX = 0.0 !
! A15 A(8,11,9) 117.1218 -DE/DX = 0.0 !
! A16 A(6,12,7) 121.4391 -DE/DX = 0.0 !
! A17 A(6,12,9) 121.4391 -DE/DX = 0.0 !
! A18 A(7,12,9) 117.1218 -DE/DX = 0.0 !
! D1 D(5,7,10,4) 0.0 -DE/DX = 0.0 !
! D2 D(5,7,10,8) 180.0 -DE/DX = 0.0 !
! D3 D(12,7,10,4) 180.0 -DE/DX = 0.0 !
! D4 D(12,7,10,8) 0.0 -DE/DX = 0.0 !
! D5 D(5,7,12,6) 0.0 -DE/DX = 0.0 !
! D6 D(5,7,12,9) 180.0 -DE/DX = 0.0 !
! D7 D(10,7,12,6) 180.0 -DE/DX = 0.0 !
! D8 D(10,7,12,9) 0.0 -DE/DX = 0.0 !
! D9 D(3,8,10,4) 0.0 -DE/DX = 0.0 !
! D10 D(3,8,10,7) 180.0 -DE/DX = 0.0 !
! D11 D(11,8,10,4) 180.0 -DE/DX = 0.0 !
! D12 D(11,8,10,7) 0.0 -DE/DX = 0.0 !
! D13 D(3,8,11,2) 0.0 -DE/DX = 0.0 !
! D14 D(3,8,11,9) 180.0 -DE/DX = 0.0 !
! D15 D(10,8,11,2) 180.0 -DE/DX = 0.0 !
! D16 D(10,8,11,9) 0.0 -DE/DX = 0.0 !
! D17 D(1,9,11,2) 0.0 -DE/DX = 0.0 !
! D18 D(1,9,11,8) 180.0 -DE/DX = 0.0 !
! D19 D(12,9,11,2) 180.0 -DE/DX = 0.0 !
! D20 D(12,9,11,8) 0.0 -DE/DX = 0.0 !
! D21 D(1,9,12,6) 0.0 -DE/DX = 0.0 !
! D22 D(1,9,12,7) 180.0 -DE/DX = 0.0 !
! D23 D(11,9,12,6) 180.0 -DE/DX = 0.0 !
! D24 D(11,9,12,7) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

Rep:Mod:dianaberheci

2018-05-10T11:29:13Z

Db2716:

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

<jmol><jmolApplet>
<title>Benzene optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DB BENZENE OPT22.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Borazine analysis===

Rep:Mod:dianaberheci

2018-05-10T11:26:51Z

Db2716: /* Benzene analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

===Borazine analysis===

Rep:Mod:dianaberheci

2018-05-10T11:25:56Z

Db2716: /* Benzene analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG
| DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

===Borazine analysis===

Rep:Mod:dianaberheci

2018-05-10T11:25:39Z

Db2716: /* Benzene analysis */

==To do list==


1. MO analysis for BH3

2. Association energy analysis + check maths

3. Vibrational analysis for BBr3, IR, compare with BH3



==BH3 optimisation==

===Optimisation===

BH3 was optimised in Gaussian using the B3LYP method and 3-21G basis set. The results of the first optimisation are included in Figure 1.

Further, a more detailed analysis was performed, using the same B3LYP method, but under the 6-31G(d,p) basis set, to yield the results in Figure 2.

{| class="wikitable" border="1"
|+
| [[File:Db fig1.PNG|650px|thumb|Figure 1: Results for 3-21G BH3 optimisation]]
|-
| [[File:Db fig2.PNG|650px|thumb|Figure 2: Results for 6-31G BH3 optimisation]]
|}

The Item table for the 6-31G(d,p) optimisation can be seen below:

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES
Predicted change in Energy=-1.635269D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.1947 -DE/DX = -0.0002 !
! R2 R(1,3) 1.1944 -DE/DX = -0.0001 !
! R3 R(1,4) 1.1948 -DE/DX = -0.0002 !
! A1 A(2,1,3) 119.9989 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0157 -DE/DX = 0.0 !
! A3 A(3,1,4) 119.9855 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The frequency analysis gave the following results:

<pre>
Low frequencies --- -2.2126 -1.0751 -0.0056 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784
</pre>

The link to the frequency log file can be found here: [[Media:Db_bh3_freq.LOG| Db_bh3_freq.LOG]]

<jmol><jmolApplet>
<title>BH3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db_bh3_freq.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrations analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A1
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|-
|2715
|126
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="1"
|+
|[[File:Db fig3.PNG|650px|thumb|Figure 3:IR spectrum for BH3]]
|}

In your wiki explain why are there less than six peaks in the spectrum, when there are obviously six vibrations.

Although there are six vibrations for the BH3 molecule, not all of them are IR active due to some vibrations not fulfilling the IR selection rule. For a vibration to be IR active, there must be a change in dipole associated with the respective vibration [r]. The IR spectrum shows only 3 peaks, associated with the active vibration modes.
The active vibrations modes are the out-of-plane symmetric bend at 1163 cm-1, the 2 degenerate bond-angle deformation asymmetric bends at 1213 cm-1 and the 2 degenerate asymmetric stretches at 2715 cm-1. The only inactive vibration mode is the symmetric stretch, as this one does not bring about any dipole moment change.
Although it seems there are in fact 5 active vibration modes, there are 2 pairs of 2 degenerate vibrations, leading to only 3 peaks on the spectrum.

===Molecular Orbitals analysis===

The Molecular Orbitals of BH3 have been computed in Gaussian. The results have been compared with the Molecular Orbital Diagram obtained through LCAO, provided by Dr. Hunt (attached below).

{| class="wikitable" border="1"
|+
|[[File:db_Bh3_mo_diagram_hunt.PNG|650px|thumb|Figure x: Molecular Orbital Diagram for BH3 [r]]]
|}

{| class="wikitable" border="1"
|+ Molecular Orbitals for BH3 computed by Gaussian compared with LCAO orbitals
! scope="col" style="width: 275px;" | Gaussian-computed Molecular Orbital snapshot
! scope="col" style="width: 100px;" | LCAO-obtained Molecular Orbital
! scope="col" style="width: 300px;" | Comparison
|-
| [[File:DbBh3 MO1.PNG|left|300px|thumb|1st MO from Gaussian]] ||The first MO not shown on the LCAO-obtained MO diagram as it is not involved in bonding ||
|-
| [[File:DbBh3 MO2.PNG|left|300px|thumb|2nd MO from Gaussian]] ||[[File:DbBh3 hunt1.PNG|left|200px|thumb|2nd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO3.PNG|left|300px|thumb|3rd MO from Gaussian]] ||[[File:DbBh3 hunt2.PNG|left|200px|thumb|3rd MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO4.PNG|left|300px|thumb|4th MO from Gaussian]] ||[[File:DbBh3 hunt3.PNG|left|200px|thumb|4th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO5.PNG|left|300px|thumb|5th MO from Gaussian]] ||[[File:DbBh3 hunt4.PNG|left|200px|thumb|5th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO6.PNG|left|300px|thumb|6th MO from Gaussian]] ||[[File:DbBh3 hunt5.PNG|left|200px|thumb|6th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO7.PNG|left|300px|thumb|7th MO from Gaussian]] ||[[File:DbBh3 hunt6.PNG|left|200px|thumb|7th MO from LCAO [r]]] ||
|-
| [[File:DbBh3 MO8.PNG|left|300px|thumb|8th MO from Gaussian]] ||[[File:DbBh3 hunt7.PNG|left|200px|thumb|8th MO from LCAO [r]]] ||
|}

==NH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig4.PNG|650px|thumb|Figure 4: Summary results for NH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-9.844604D-11
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.018 -DE/DX = 0.0 !
! R2 R(1,3) 1.018 -DE/DX = 0.0 !
! R3 R(1,4) 1.018 -DE/DX = 0.0 !
! A1 A(2,1,3) 105.7446 -DE/DX = 0.0 !
! A2 A(2,1,4) 105.7446 -DE/DX = 0.0 !
! A3 A(3,1,4) 105.7446 -DE/DX = 0.0 !
! D1 D(2,1,4,3) -111.8637 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:DB NH3 FREQ.LOG| DB NH3 FREQ.LOG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

==NH3BH3 optimisation==

{| class="wikitable" border="1"
|+
|[[File:Db fig5.PNG|650px|thumb|Figure 5: Summary results for NH3BH3]]
|}

The Item table can be seen below:

<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
Predicted change in Energy=-1.631175D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,7) 1.21 -DE/DX = -0.0001 !
! R2 R(2,7) 1.21 -DE/DX = -0.0001 !
! R3 R(3,7) 1.21 -DE/DX = -0.0001 !
! R4 R(4,8) 1.0186 -DE/DX = -0.0001 !
! R5 R(5,8) 1.0186 -DE/DX = -0.0001 !
! R6 R(6,8) 1.0186 -DE/DX = -0.0001 !
! R7 R(7,8) 1.6681 -DE/DX = -0.0001 !
! A1 A(1,7,2) 113.8743 -DE/DX = 0.0 !
! A2 A(1,7,3) 113.8743 -DE/DX = 0.0 !
! A3 A(1,7,8) 104.5972 -DE/DX = 0.0 !
! A4 A(2,7,3) 113.874 -DE/DX = 0.0 !
! A5 A(2,7,8) 104.5968 -DE/DX = 0.0 !
! A6 A(3,7,8) 104.5969 -DE/DX = 0.0 !
! A7 A(4,8,5) 107.8685 -DE/DX = 0.0 !
! A8 A(4,8,6) 107.8685 -DE/DX = 0.0 !
! A9 A(4,8,7) 111.0294 -DE/DX = 0.0 !
! A10 A(5,8,6) 107.8686 -DE/DX = 0.0 !
! A11 A(5,8,7) 111.0303 -DE/DX = 0.0 !
! A12 A(6,8,7) 111.0302 -DE/DX = 0.0 !
! D1 D(1,7,8,4) 179.9998 -DE/DX = 0.0 !
! D2 D(1,7,8,5) -60.0003 -DE/DX = 0.0 !
! D3 D(1,7,8,6) 60.0001 -DE/DX = 0.0 !
! D4 D(2,7,8,4) -60.0 -DE/DX = 0.0 !
! D5 D(2,7,8,5) 59.9998 -DE/DX = 0.0 !
! D6 D(2,7,8,6) -179.9998 -DE/DX = 0.0 !
! D7 D(3,7,8,4) 59.9997 -DE/DX = 0.0 !
! D8 D(3,7,8,5) 179.9995 -DE/DX = 0.0 !
! D9 D(3,7,8,6) -60.0001 -DE/DX = 0.0 !
--------------------------------------------------------------------------------
</pre>

The link to the frequency log file can be found here: [[Media:Db NH3BH3 FREQ.LOG| Db NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.0007 0.0009 0.0015 13.6144 18.8476 42.5238
Low frequencies --- 266.2562 632.2749 639.0335
</pre>

==Association Energy==

ENH3=-56.55776 a.u.

EBH3=-26.61532 a.u.

ENH3BH3=-83.22468 a.u.



<math>\Delta E = E_{NH_3BH_3}-(E_{NH_3}+E_{BH_3})</math>

<math>\Delta E = -0.0516 a.u. </math>

<math>\Delta E = 32.379 kJ/mol </math>

Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?

==BBr3 optimisation==

{| class="wikitable"
|+
|[[File:Db Bbr3 scanthingie summtable.PNG|650px|thumb|Figure 6: Summary results for BBr3]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
Predicted change in Energy=-4.026879D-10
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.934 -DE/DX = 0.0 !
! R2 R(1,3) 1.934 -DE/DX = 0.0 !
! R3 R(1,4) 1.934 -DE/DX = 0.0 !
! A1 A(2,1,3) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,4) 120.0 -DE/DX = 0.0 !
! A3 A(3,1,4) 120.0 -DE/DX = 0.0 !
! D1 D(2,1,4,3) 180.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:Db bbr3 log.LOG| Db bbr3 log.LOG]]

<pre>
Low frequencies --- -0.0116 -0.0065 -0.0004 49.9507 49.9507 50.0316
Low frequencies --- 144.7605 144.7639 215.6179
</pre>

<jmol><jmolApplet>
<title>BBr3 optimised molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Db bbr3 log.LOG</uploadedFileContents>
</jmolApplet></jmol>

The link to the DOI of the analysis for this molecule can be found here: {{DOI|10042/202358}}

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|145
|0.09
|E
|no
|bend
|-
|145
|0.09
|E
|no
|bend
|-
|216
|0
|A1
|no
|symmetric stretch
|-
|407
|5
|A1
|slightly
|out-of-plane bend
|-
|622
|313
|E
|yes
|asymmetric stretch
|-
|622
|313
|E
|yes
|asymmetric stretch
|}

{| class="wikitable" border="0"
|+
|[[File:DbBbr3 ir.PNG|650px|thumb|Figure :IR spectrum for BBr3]]
|}

==Project: Aromaticity==

===Benzene analysis===
{| class="wikitable"
|+
|[[File:Db benzene goodsummary.PNG|650px|thumb|Figure :Summary table for optimised benzene]]
|}

<pre>
Item Value Threshold Converged?
Maximum Force 0.000194 0.000450 YES
RMS Force 0.000077 0.000300 YES
Maximum Displacement 0.000824 0.001800 YES
RMS Displacement 0.000289 0.001200 YES
Predicted change in Energy=-4.246203D-07
Optimization completed.
-- Stationary point found.
----------------------------
! Optimized Parameters !
! (Angstroms and Degrees) !
-------------------------- --------------------------
! Name Definition Value Derivative Info. !
--------------------------------------------------------------------------------
! R1 R(1,2) 1.3962 -DE/DX = 0.0001 !
! R2 R(1,6) 1.3962 -DE/DX = 0.0001 !
! R3 R(1,7) 1.0861 -DE/DX = 0.0002 !
! R4 R(2,3) 1.3962 -DE/DX = 0.0001 !
! R5 R(2,8) 1.0861 -DE/DX = 0.0002 !
! R6 R(3,4) 1.3962 -DE/DX = 0.0001 !
! R7 R(3,9) 1.0861 -DE/DX = 0.0002 !
! R8 R(4,5) 1.3962 -DE/DX = 0.0001 !
! R9 R(4,10) 1.0861 -DE/DX = 0.0002 !
! R10 R(5,6) 1.3962 -DE/DX = 0.0001 !
! R11 R(5,11) 1.0861 -DE/DX = 0.0002 !
! R12 R(6,12) 1.0861 -DE/DX = 0.0002 !
! A1 A(2,1,6) 120.0 -DE/DX = 0.0 !
! A2 A(2,1,7) 120.0 -DE/DX = 0.0 !
! A3 A(6,1,7) 120.0 -DE/DX = 0.0 !
! A4 A(1,2,3) 120.0 -DE/DX = 0.0 !
! A5 A(1,2,8) 120.0 -DE/DX = 0.0 !
! A6 A(3,2,8) 120.0 -DE/DX = 0.0 !
! A7 A(2,3,4) 120.0 -DE/DX = 0.0 !
! A8 A(2,3,9) 120.0 -DE/DX = 0.0 !
! A9 A(4,3,9) 120.0 -DE/DX = 0.0 !
! A10 A(3,4,5) 120.0 -DE/DX = 0.0 !
! A11 A(3,4,10) 120.0 -DE/DX = 0.0 !
! A12 A(5,4,10) 120.0 -DE/DX = 0.0 !
! A13 A(4,5,6) 120.0 -DE/DX = 0.0 !
! A14 A(4,5,11) 120.0 -DE/DX = 0.0 !
! A15 A(6,5,11) 120.0 -DE/DX = 0.0 !
! A16 A(1,6,5) 120.0 -DE/DX = 0.0 !
! A17 A(1,6,12) 120.0 -DE/DX = 0.0 !
! A18 A(5,6,12) 120.0 -DE/DX = 0.0 !
! D1 D(6,1,2,3) 0.0 -DE/DX = 0.0 !
! D2 D(6,1,2,8) 180.0 -DE/DX = 0.0 !
! D3 D(7,1,2,3) 180.0 -DE/DX = 0.0 !
! D4 D(7,1,2,8) 0.0 -DE/DX = 0.0 !
! D5 D(2,1,6,5) 0.0 -DE/DX = 0.0 !
! D6 D(2,1,6,12) 180.0 -DE/DX = 0.0 !
! D7 D(7,1,6,5) 180.0 -DE/DX = 0.0 !
! D8 D(7,1,6,12) 0.0 -DE/DX = 0.0 !
! D9 D(1,2,3,4) 0.0 -DE/DX = 0.0 !
! D10 D(1,2,3,9) 180.0 -DE/DX = 0.0 !
! D11 D(8,2,3,4) 180.0 -DE/DX = 0.0 !
! D12 D(8,2,3,9) 0.0 -DE/DX = 0.0 !
! D13 D(2,3,4,5) 0.0 -DE/DX = 0.0 !
! D14 D(2,3,4,10) 180.0 -DE/DX = 0.0 !
! D15 D(9,3,4,5) 180.0 -DE/DX = 0.0 !
! D16 D(9,3,4,10) 0.0 -DE/DX = 0.0 !
! D17 D(3,4,5,6) 0.0 -DE/DX = 0.0 !
! D18 D(3,4,5,11) 180.0 -DE/DX = 0.0 !
! D19 D(10,4,5,6) 180.0 -DE/DX = 0.0 !
! D20 D(10,4,5,11) 0.0 -DE/DX = 0.0 !
! D21 D(4,5,6,1) 0.0 -DE/DX = 0.0 !
! D22 D(4,5,6,12) 180.0 -DE/DX = 0.0 !
! D23 D(11,5,6,1) 180.0 -DE/DX = 0.0 !
! D24 D(11,5,6,12) 0.0 -DE/DX = 0.0 !
--------------------------------------------------------------------------------

</pre>

The link to the frequency log file can be found here: [[Media:DB BENZENE OPT22.LOG
|DB BENZENE OPT22.LOG]]

<pre>
Low frequencies --- -2.1456 -2.1456 -0.0088 -0.0042 -0.0041 10.4835
Low frequencies --- 413.9768 413.9768 621.1390
</pre>

===Borazine analysis===

File:DB BENZENE OPT22.LOG

2018-05-10T11:24:40Z

Db2716: