View source for KG971003

== EX<sub>3</sub> project ==

== BH<sub>3</sub> ==

=== Optimisation ===

• Method:RB3LYP

• Basis set:6-31G

[[File:Gzy bh3 opt 631g.PNG]]

•E=-26.61532 a.u.

<pre>
 Item               Value     Threshold  Converged?
 Maximum Force            0.000192     0.000450     YES
 RMS     Force            0.000126     0.000300     YES
 Maximum Displacement     0.000763     0.001800     YES
 RMS     Displacement     0.000500     0.001200     YES
</pre>

•link to frequency .log file:
[[Media:GZY_BH3_FREQ.LOG|GZY_BH3_FREQ.LOG]]

<pre>
Low frequencies ---   -0.2263   -0.1037   -0.0054   47.9770   49.0378   49.0383
 Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><jmolApplet>
  <title>BH3</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>GZY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+ 
|-
|wavenumber (cm<sup>-1</sup>) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|92
|A<sub>1</sub>
|yes
|out-of-plane bend
|-
|1213
|14
|E
|slight
|bend
|-
|1213
|14
|E
|slight
|bend
|-
|2579
|0
|A<sub>1</sub>
|no
|symmetric stretch
|-
|2712
|126
|E
|yes
|asymmetric stretch
|-
|2712
|126
|E
|yes
|asymmetric stretch
|}

[[File:Gzy spectrum.PNG]]

•There are only 3 peaks visible in the spectrum, which is fewer than 6 peaks derived from 3N-6 rule. The reason is that some of the vibrations are not IR active, such as the symmetric stretch. In addition to that, there are two vibrations with the same frequency, this lead to the overlap of two peaks to give a larger one.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:07, 30 May 2018 (BST) Which vibrations are inactive, and which ones are degenerate? Be more specific. Otherwise, good!

=== MO diagram for BH<sub>3</sub> ===

[[File:Gzy annotated MO.PNG]]

          Lecture 4 Tutorial Problem Model Answers from Dr. Patricia Hunt

•There are not many significant differences between the real and LCAO MOs. This shows that the qualitative MO theory is accurate and useful.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:08, 30 May 2018 (BST) Are there ''any'' differences?

== Association energy ==

=== NH<sub>3</sub> optimisation ===

[[File:Gzy nh3summary.PNG]]


=== NH<sub>3</sub>BH<sub>3</sub> optimisation ===

[[File:Gzy nh3bh3summary.PNG]]

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:09, 30 May 2018 (BST) You're missing the remaining information (log files, etc.) for these calculations. 

ΔE = E(NH<sub>3</sub>BH<sub>3</sub>) - [E(NH<sub>3</sub>)+E(BH<sub>3</sub>)] = -0.05159678 a.u.= -135 kJ/mol

•It is a sensible value. Normal covalent single bond strength is between 200-500 kJ/mol. This is a weak dative bond because it is much weaker than C-C bond which is about 350 kJ/mol.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:09, 30 May 2018 (BST) Remember to cite a literature value for your bond enthalpy (ideally from a paper source).

== BBr<sub>3</sub> ==

=== Optimisation ===

•Method:RB3LYP

•Basis set:Gen

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:10, 30 May 2018 (BST) Be careful here. "Gen" is not a valid descriptor for this basis set. You actually mean something like LANL2DZ/6-31G(d,p)

[[File:Gzy bbr3 summary.PNG]]

<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
</pre>

=== Frequency analysis ===

[[File:Gzy bbr3 freq1 summary.PNG]]

<pre>
        Item               Value     Threshold  Converged?
 Maximum Force            0.000008     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000036     0.001800     YES
 RMS     Displacement     0.000018     0.001200     YES
</pre>

<pre>
Low frequencies ---   -0.0137   -0.0064   -0.0046    2.4315    2.4315    4.8421
Low frequencies ---  155.9631  155.9651  267.7052
</pre>

{{DOI|10042/202425}}

== Benzene and Borazine ==

=== Benzene optimisation ===

•Method:RB3LYP

•Basis set:6-31G

[[File:Gzy benzene optsummary.PNG]]

<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
</pre>

=== Benzene frequency analysis ===

•Method:RB3LYP

•Basis set:6-31G

[[File:Gzy benzene freqsummary.PNG]]

<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000198     0.000450     YES
 RMS     Force            0.000087     0.000300     YES
 Maximum Displacement     0.000757     0.001800     YES
 RMS     Displacement     0.000321     0.001200     YES

</pre>

<pre>
Low frequencies ---   -2.1456   -2.1456   -0.0088   -0.0043   -0.0042   10.4835
Low frequencies ---  413.9768  413.9768  621.1390
</pre>

•IR spectrum---all positive

[[File:Gzy benzene ir.PNG]]

•Jmol image of Benzene

<jmol><jmolApplet>
  <title>Benzene</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>GZY BENZENE FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:GZY BENZENE FREQ.LOG | GZY BENZENE FREQ.LOG]]

=== Borazine optomisation ===

•Method:RB3LYP

•Basis set:6-31G

[[File:Gzy borazine optsummary.PNG]]

<pre>
        Item               Value     Threshold  Converged?
 Maximum Force            0.000068     0.000450     YES
 RMS     Force            0.000037     0.000300     YES
 Maximum Displacement     0.000409     0.001800     YES
 RMS     Displacement     0.000136     0.001200     YES

</pre>

=== Borazine frequency analysis ===

•Method:RB3LYP

•Basis set:6-31G

[[File:Gzy borazine freqsummary.PNG]]

<pre>
        Item               Value     Threshold  Converged?
 Maximum Force            0.000201     0.000450     YES
 RMS     Force            0.000067     0.000300     YES
 Maximum Displacement     0.000448     0.001800     YES
 RMS     Displacement     0.000179     0.001200     YES
</pre>

<pre>
Low frequencies ---  -11.1371  -10.9083  -10.7025   -0.0104   -0.0093    0.0939
Low frequencies ---  289.1003  289.1090  403.9346
</pre>

•IR spectrum-- all positive

[[File:Gzy borazine ir.PNG]]

•Jmol image of borazine

<jmol><jmolApplet>
  <title>Benzene</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>GZY BORAZINE FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

[[Media:GZY BORAZINE FREQ.LOG | GZY BORAZINE FREQ.LOG]]

=== Charge analysis ===

[[File:Gzy benzene cd.PNG|310px]]
[[File:Gzy borazine cd.PNG|300px]]

Charge distribution of Benzene(left) and Borazine(right)

• Charge analysis benzene

{| class="wikitable"
|+ 
|-
|'''Benzene'''  || '''Electronegativity''' || '''Charge / a.u.'''
|-
|C
|2.5
| -0.239
|-
|H
|2.1
| +0.239
|}

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:12, 30 May 2018 (BST) Remember to use the same colour scale for both molecules. 

• Charge analysis borazine

{| class="wikitable"
|+ 
|-
|'''Borazine'''  || '''Electronegativity''' || '''Charge / a.u.'''
|-
|N
|3.0
| -1.102
|-
|B
|2.0
| +0.747
|-
|H-N
|2.1
| +0.432
|-
|H-B
|2.1
| -0.077
|}


-The charge distribution is dependent on the electronegativity of atoms in Benzene and Borazine.

-In Benzene, C is more electronegative than H, resulting in a greater electron density around C. This leads to the positive charge on H and negative charge on C.

-In Borazine, N is the most electronegative atom, therefore, the electron density around N is the greatest. This is consistent with the most negative charge on N which is -1.102 au. As H has a slight larger electronegativity than B, H atom connected to B have a slightly negative charge which means B-H bond is less polarised, while those connected to N is positively charged which lead to a more polarized N-H bond.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:13, 30 May 2018 (BST) Good discussion of the effects of electronegativity on the overall charge distribution but more discussion is needed. What do the partial charges sum to, and is there any difference in partial charge for atoms related by symmetry?

=== MOs comparison ===

{| class="wikitable"
|+ 
|-
|'''Benzene'''  || '''Borazine''' || '''Description'''
|-
|[[File:Gzy benzene 14.PNG]]
|[[File:Gzy borazine 15.PNG]]
|This is the 14th MO of Benzene compared to the 15th MO of Borazine. Both orbitals are the anti-bonding orbitals but with slightly different energies. Both molecular orbitals have a C3 rotational axis perpendicular to the plane containing both molecules. The MO of Benzene should be more symmetric compared to that of Borazine due to the larger difference in electronegativity in Borazine. The MO diagram indicates a larger electron density around Nitrogen.
|-
|[[File:Gzy benzene 17.PNG|225px]]
|[[File:Gzy borazine 17.PNG]]
|This is the 17th MO of Benzene compared to the 17th MO of Borazine. MO 17 is the bonding pi orbital for both benzene and borazine. The difference in symmetry is more obvious in this pair. The MO of benzene is symmetric with a C6 rotational axis perpendicular to the plane containing benzene while the MO of borazine is less symmetric with a large contribution by nitrogen atom due to the large electronegativity of nitrogen atoms.
|-
|[[File:Gzy benzene 21.PNG|225px]]
|[[File:Gzy borazine 21.PNG]]
|This is the 21th MO of Benzene compared to the 21th MO of Borazine. MO 21 is the anti-bonding pi orbital for both complexes. The MO for benzene is symmetric with a C2 rotational axis parallel to the plane containing the molecule. In borazine, the smaller orbitals at the upper part is due to the high electronegativity of nitrogen. 
|}

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:15, 30 May 2018 (BST) Well done for comparing the correct MOs by shape and not energetic ordering (which is not necessarily reliable). I would include a brief discussion of the overall symmetry and perhaps a more detailed discussion of the differences between the molecules to improve this section further. Perhaps also consider dicussing the constituent AOs that form the MOs and the overall symmetry of the MO.

=== Aromaticity ===

At first, aromaticity is related to Benzene. Aromaticity is usually used to describe a cyclic, planar molecule with the number of resonace bonds obeying Hackle's law and is more stable than other geometry with the same set of atoms.  The stability is due to the delocalised system of pi orbitals as a result of pz orbital overlapping as shown in Benzene MO diagram above. In Borazine, the overlap is between hetroatoms. ie. nitrogen and Boron. The difference in energy and electronegativity can result in distortion of the pi system.

However, it is now well known that aromaticity can also be applied on non-planar molecules because the planrity can be destroyed easily, eg, benzene adopts a chair conformation in crystalline state at 20K. A good way to investigate the pi system is the Bader quantum theory atons in molecules.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:20, 30 May 2018 (BST) How is aromaticity maintained upon the destruction of planarity? Can you find aromaticity in other non-planar molecules? What other modern perspectives on aromaticity are there. What you have written is correct, but overall more discussion is needed. 

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 18:20, 30 May 2018 (BST) Some good aspects of this report. However, the level of detail in your discussion (especially in the second section) should be much greater. You have performed your calculations correctly and obtained good results, but you need to analyse them in greater depth.