ChemWiki - User contributions [en]

Inorganic:sherryqw1998

2019-05-15T14:34:27Z

Zl6217: /* BH3 molecule */

== BH3 molecule ==

'''The method and basis set:''' B3LYP/6-31G level

'''Summary table:'''

[[File:Summary sherryzl.PNG]]

'''Item table:'''
<pre>
Item Value Threshold Converged?
Maximum Force 0.000018 0.000450 YES
RMS Force 0.000009 0.000300 YES
Maximum Displacement 0.000070 0.001800 YES
RMS Displacement 0.000035 0.001200 YES
</pre>

'''Frequency analysis log file:'''

[[Media:Lz3717_BH3_FREQ.LOG| BH3_frequency.log]]

'''Low frequencies table:'''
<pre>
Low frequencies --- -10.3498 -3.4492 -1.2454 -0.0056 0.4779 3.2165
Low frequencies --- 1162.9519 1213.1527 1213.1554
</pre>

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Lz3717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''Information about BH3 vibrations:'''
{| class="wikitable" border="1"
|+ BH3 vibration
! Mode !! wavenumber(cm-1) !! Intensity !! Symmetry !! Dipole moment(Deby) !! IR active? !! Types of vibrations
|-
| 1 || 1163 || 317 || A2'' || 92.55 || yes || out-of-plane bend
|-
| 2 || 1213 || 46 || E' || 14.05 || yes || bend
|-
| 3 || 1213 || 46 || E' || 14.06 || yes || bend
|-
| 4 || 2582 || 0 || A1' || 0.00 || no || symmetric stretch
|-
| 5 || 2716 || 186 || E' || 126.32 || yes || asymmetric stretch
|-
| 6 || 2716 || 186 || E' || 126.32 || yes || symmetric stretch
|}

'''BH3 IR spectrum:'''

[[File:BH3 IR LZ3717.PNG]]

'''Explanation of IR spectrum:'''

There are overall 6 vibration modes of BH3, but only 4 peaks can be seen on the IR. Mode 2 and 3 have the same wavenumbers and intensities, so there is only one peak shown on the IR because these two peaks overlap. So as mode 5 and 6. Mode 4 does not have the change in dipole, so it is IR inactive, no peak can be seen on the IR.

'''The MO diagram of BH3:'''

[[File:MO-ZL-BH3 TOTAL.PNG]]
<ref name="HuntResearchGroup" />
<references>
<ref name="HuntResearchGroup">This is HuntResearchGroup reference.</ref>
</references>

'''Questions:'''

'''1.Are there any significant differences between the real and LCAO MOs?'''

The LCAO MOs only show the individual AO components which can be used for predictions theoretically. However the real model gives the exact size of AOs for different elements and how the mix looks like in reality.

'''2.What does this say about the accuracy and usefulness of qualitative MO theory?'''

Compared to the real situation and LCAO MOs, the LCAO MOs theory correspond to the real, which is useful for the predictions.

==Association energies: Ammonia-Borane==

'''The energy of the dissociated fragments:'''

E(NH3)=-56.55664 a.u.

E(BH3)=-26.61532 a.u.

E(NH3BH3)=-83.18368 a.u.

'''The association energy:'''

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]= -83.18368 a.u. + 26.61532 a.u. + 56.55664 a.u. = -0.01172 a.u. = -31 kJ/mol

'''Question:'''

'''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?'''

Compared to the bond strength of C-C bond, which is 346 kJ/mol, the bond strength of B-N bond is much smaller than that of C-C bond. It means that the B-N dative bond is weak.

Cyn6217

2019-05-10T16:23:02Z

Zl6217: /* Profile of BH3 (Boron Hydride) */

== Molecule modelling and Analysis ==

== The profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

'''IR spectrum'''

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = -(E(NH3BH3)-(E(NH3)+E(BH3))) = -0.052 a.u. = -136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:22:05Z

Zl6217: /* charge distribution */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

'''IR spectrum'''

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = -(E(NH3BH3)-(E(NH3)+E(BH3))) = -0.052 a.u. = -136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:20:53Z

Zl6217: /* The association energy of NH3 BH3 (Ammonia Boron) */

Cyn6217

2019-05-10T16:19:00Z

Zl6217: /* Profile of BH3 (Boron Hydride) */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

'''IR spectrum'''

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:18:10Z

Zl6217: /* Profile of BH3 (Boron Hydride) */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

'''IR spectrum'''
In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:17:03Z

Zl6217: /* Visualisation of valence MOs of N(CH3)4+ */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:16:39Z

Zl6217: /* Visualisation of valence MOs of N(CH3)4+ */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:16:20Z

Zl6217: /* Visualisation of valence MOs of N(CH3)4+ */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:15:27Z

Zl6217: /* The association energy of NH3 BH3 (Ammonia Boron) */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybride and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy absorbed to break a bond
While association energy is ,in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with a stable B-N bond's energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could be easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:11:58Z

Zl6217: /* The association energy of NH3 BH3 (Ammonia Boron) */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy needed to break a bond
While association energy is in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with B-N bond energy (377.9 kJ/mol [1]). It can be said to be a weak bond so that the bond could easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:11:26Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy needed to break a bond
While association energy is in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with B-N bond energy (377.9 kJ/mol). It can be said to be a weak bond so that the bond could easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

==Reference==

1. Unkonwn Author Staff.ustc.edu.cn. (2019). [online] Available at: http://staff.ustc.edu.cn/~luo971/2010-91-CRC-BDEs-Tables.pdf [Accessed 10 May 2019].

Cyn6217

2019-05-10T16:05:44Z

Zl6217: /* The association energy of NH3 BH3 (Ammonia Boron) */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy needed to break a bond
While association energy is in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with B-N bond energy (377.9 kJ/mol). It can be said to be a weak bond so that the bond could easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T16:05:18Z

Zl6217: /* The association energy of NH3 BH3 (Ammonia Boron) */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Bond energy is the energy needed to break a bond
While association energy is in general, the energy emitted while two groups are associated,which might not as strong as the bond energy in this case.
I compared B-N association energy with B-N bond energy (377.9). It can be said to be a weak bond so that the bond could easily dissociate.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:53:01Z

Zl6217: /* charge distribution */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:51:01Z

Zl6217: /* charge distribution */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH<sub>3</sub>)<sup>4+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sup>4+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:50:36Z

Zl6217: /* charge distribution */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(<sub>CH3</sub>)<sup>4+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH<sub>3</sub>)<sup>4+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:49:06Z

Zl6217: /* charge distribution */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+</sup> P(CH3)<sup>4+</sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:48:35Z

Zl6217: /* charge distribution */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+</sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+</sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:46:49Z

Zl6217: /* Ionic Liquids: Designer Solvents */

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized.

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:45:59Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:45:16Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:44:31Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''
This orbital is with all bonding interactions between AOs. It is a MO consists of p orbital of Cs and 2 s orbitals on Hs. All the orbitals overlap with the same phase as itself.

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''
There is anti-bonding through space between the neighbouring p orbitals which will higher the energy and destabilized the overall structure. Meanwhile, in the methyl group, there's bonding overlap between s orbitals and the p orbtial which lies in the same plane with them.
[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''
This orbital mainly shows bonding character since all the p orbitals overlap with each other in a parallel orientation and the overlap areas are with the same phase. In the methyl group, the bonding character dominates as well.

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:31:17Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P < H < C. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N > C > H because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:28:10Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)<sub>4</sub>]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P (2.19) < H (2.20)< C(2.55)[2]. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N (3.04) > C (2.55) > H (2.20) [2] because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sub>4</sub><sup>+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

Cyn6217

2019-05-10T15:25:11Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)4]<sup>+</sup>==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)<sub>4+</sub>]<sup>+</sup> ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)<sup>4+<sup>'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)<sup>4+<sup>'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)<sup>4+<sup> P(CH3)<sup>4+<sup>
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)<sup>4+</sup> cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P (2.19) < H (2.20)< C(2.55)[2]. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)<sub>4+</sub> cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N (3.04) > C (2.55) > H (2.20) [2] because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)<sub>4</sub>]+ since it was N carries all the positive formal charge instead of all the Hs.

==Visualisation of valence MOs of N(CH3)<sup>4+</sup>==

In this section, the MOs of this cation was vistualised with gaussian after frequency anaylsis. Overall, the bonding character dominate the filled orbitals when some anti-bonding between space etc. could be observed in several orbitals.

'''1.Orbital 14'''

[[File:Orbital 14.PNG|250px]][[File:Orbital 14 1.PNG|650px]]

'''2.Orbital 18'''

[[File:Orbital 18.PNG|250px]][[File:Orbital 18 1.PNG|650px]]

'''3.Orbital 20'''

[[File:Orbital 20.PNG|250px]][[File:Orbital 20 1.PNG|650px]]

File:Orbital 20.PNG

2019-05-10T15:05:57Z

Zl6217:

File:Orbital 20 1.PNG

2019-05-10T15:05:20Z

Zl6217:

File:Orbital 18.PNG

2019-05-10T15:04:54Z

Zl6217:

File:Orbital 18 1.PNG

2019-05-10T15:04:23Z

Zl6217:

File:Orbital 14.PNG

2019-05-10T15:03:54Z

Zl6217:

File:Orbital 14 1.PNG

2019-05-10T15:02:19Z

Zl6217:

Cyn6217

2019-05-10T12:39:37Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)4]+==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)4]+ ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)4+'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)4+'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)4+ cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P (2.19) < H (2.20)< C(2.55)[2]. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)4+ cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N (3.04) > C (2.55) > H (2.20) [2] because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy. The negative charge n C is higher than N probably because the occupied MOs were with energy level which is closer to the C atom’s energy level, therefore C AOs have larger contribution to the MOs, more electron density is closer to C.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)4]+ since it was N carries all the positive formal charge instead of all the Hs.

Cyn6217

2019-05-10T12:19:01Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

In this section, the charge distribution of two cations used in the ionic liquid was investigated. As a room-temperature liquid composed purely of ions, the ions are required to be charge-delocalized. [3]

== The profile of [P(CH3)4]+==

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of [N(CH3)4]+ ==

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''The charge distribution of cation P(CH3)4+'''

[[File:P charge.PNG|500px]]

'''The charge distribution of cation N(CH3)4+'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)4+ cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P (2.19) < H (2.20)< C(2.55)[2]. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)4+ cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N (3.04) > C (2.55) > H (2.20) [2] because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)4]+ since it was N carries all the positive formal charge instead of all the Hs.

Cyn6217

2019-05-10T12:10:43Z

Zl6217:

== Molecule modelling and Analysis ==

== Profile of BH<sub>3 </sub> (Boron Hydride) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== The profile of NH<sub>3 </sub> (Ammonia) ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

'''Frequency analysis log file'''

[[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The profile of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

'''Frequency analysis log file'''
[[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== The association energy of NH<sub>3 </sub>BH<sub>3 </sub> (Ammonia Boron)==

After frequency analysis to calculate the minimum energy of ammonia, boron hybrids and Ammonia Boron, the B-N association bond energy could be calculated with equation : association energy = E(NH3BH3)-(E(NH3)+E(BH3)))
E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-(E(NH3)+E(BH3))) = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol[1]). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''P(CH3)4+'''

[[File:P charge.PNG|500px]]

'''N(CH3)4+'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.

For P(CH3)4+ cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This distribution is generally consistent with the relative electronegativity of P, C and H : P (2.19) < H (2.20)< C(2.55)[2]. P was with the lowest electronegativity, it has weak ability to attract electron ,therefore, it carries the largest positive charge. In addition, the effective nuclear charge could also influence the positive charge carried by each atom. P have the largest positive charge can also due to its large nuclear charge (+15). The low positive charge of H can probably be justified since its effective nuclear charge was originally small.

For N(CH3)4+ cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs. This can be justified by the relative electronegativity of N,C and H: N (3.04) > C (2.55) > H (2.20) [2] because more electronegative atom trends to attract electron density, making its partial charge more negative. This is corresponding to the MO diagram in the MO diagram, the energy level of more electronegative element is relatively lower and more available for electrons to occupy.

These data was contradict to the communal traditional description of the formal charge location on [N(CH3)4]+ since it was N carries all the positive formal charge instead of all the Hs.

Cyn6217

2019-05-10T11:14:38Z

Zl6217:

Cyn6217

2019-05-10T10:48:40Z

Zl6217:

== BH<sub>3 </sub>Boron Hydride ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== NH<sub>3 </sub> Ammonia ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== the association energy of NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==

E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-[E(NH3)+E(BH3)] = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

'''P(CH3)4+'''

[[File:P charge.PNG|500px]]

'''N(CH3)4+'''

[[File:N charge.PNG|500px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Overall, both cations carries +1 charge.
For P(CH3)4+ cation, P atom carries most of the positive charge (1.667). Meanwhile, all the carbon atoms have equally positive charge 1.060 and hydrogen atoms also shares identical +0.298 charge. The distribution of the positive charge is evenly descending from the central atom P. This character can be justified since it is the most electronegative element, molecule could be stabilized more if the more electronegative element carries most of the charges

For N(CH3)4+ cation, conversely N carries negative charge (-0.295) while Cs also have negative charge: -0.483. All the positive charge was evenly distributed among Hs (0.269). In summary, the charge was increasing from the central ion to the Hs.

Cyn6217

2019-05-09T16:04:38Z

Zl6217:

== BH<sub>3 </sub>Boron Hydride ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== NH<sub>3 </sub> Ammonia ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== the association energy of NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==

E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-[E(NH3)+E(BH3)] = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

P(CH3)4+
[[File:P charge.PNG|250px]]

N(CH3)4+
[[File:N charge.PNG|250px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Both molecules carry +1 charge, the charge distribution depends on

Cyn6217

2019-05-09T15:55:42Z

Zl6217:

== BH<sub>3 </sub>Boron Hydride ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== NH<sub>3 </sub> Ammonia ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== the association energy of NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==

E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-[E(NH3)+E(BH3)] = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

P(CH3)4+
[[File:P charge.PNG|250px]]

N(CH3)4+
[[File:N charge.PNG|250px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Cyn6217

2019-05-09T15:37:15Z

Zl6217:

== BH<sub>3 </sub>Boron Hydride ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== NH<sub>3 </sub> Ammonia ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== the association energy of NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==

E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-[E(NH3)+E(BH3)] = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

P(CH3)4+
[[File:P charge.PNG|250px]]

N(CH3)4+
[[File:N charge.PNG|250px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

File:P charge.PNG

2019-05-09T15:33:56Z

Zl6217:

File:N charge.PNG

2019-05-09T15:33:26Z

Zl6217: Zl6217 uploaded a new version of File:N charge.PNG

File:N charge.PNG

2019-05-09T15:32:38Z

Zl6217:

Cyn6217

2019-05-09T15:32:21Z

Zl6217:

== BH<sub>3 </sub>Boron Hydride ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== NH<sub>3 </sub> Ammonia ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== the association energy of NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==

E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-[E(NH3)+E(BH3)] = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:NNR4 summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000887 0.001800 YES
RMS Displacement 0.000433 0.001200 YES
</pre>

Frequency analysis log file [[Media:-NN(CH3)4-+ FRE.LOG]]

<pre>
Low frequencies --- -0.0004 0.0003 0.0003 34.6230 34.6230 34.6230
Low frequencies --- 216.8782 316.1696 316.1696
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>-NN(CH3)4-+ FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==charge distribution==

[[File:NNR4 summary.PNG|250px]]

[[File:NNR4 summary.PNG|250px]]
<pre>
N(CH3)4+ P(CH3)4+
H 0.269 0.296
C -0.483 -1.060
N/P -0.295 1.667
</pre>

Cyn6217

2019-05-09T15:22:12Z

Zl6217:

Cyn6217

2019-05-09T15:18:49Z

Zl6217:

File:-NN(CH3)4-+ FRE.LOG

2019-05-09T15:10:26Z

Zl6217:

File:NNR4 summary.PNG

2019-05-09T15:09:13Z

Zl6217:

Cyn6217

2019-05-09T15:08:39Z

Zl6217:

== BH<sub>3 </sub>Boron Hydride ==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000189 0.000450 YES
RMS Force 0.000095 0.000300 YES
Maximum Displacement 0.000746 0.001800 YES
RMS Displacement 0.000373 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2263 -0.1037 -0.0055 47.9770 49.0378 49.0383
Low frequencies --- 1163.7209 1213.6704 1213.6731
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<pre>
vibration 1 2 3
symmetry A2" E' E'
Frequencies 1163.7209 1213.6704 1213.6731
IR Intensity 92.4742 14.0889 14.0925

vibration 4 5 6
symmetry A1' E' E'
Frequencies 2579.7463 2712.6720 2712.6731
IR Inten 0.0000 126.4183 126.4087
</pre>

[[File:Bh3zylir.PNG|650px]]

In the IR spectrum above, there were only 3 peaks shown while there are in total 6 vibration modes. It is because that 1. vibration 2 and 3, vibration 5 and 6 have same frequencies, so the peaks overlap with each other; 2. the vibration 4 is symmetrical, hence it is not IR active.

'''MO diagram'''

[[File:MO DIAGRAM.PNG|550px]]

Compared with the real MO diagrams, the LCAOS show consistent bonding and anti-bonding phases and similar extent of contribution of each AO to MO;
Therefore, the qualitative MO theory provides a proper superficial approximation of the shapes and charge distributions of MOs. However, the exact c constant values, energy and size of the MO still require further calculation with Schrodinger’s equation and optimization.

== NH<sub>3 </sub> Ammonia ==
'''B3LYP/6-31G(d,p) level'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000092 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000304 0.001800 YES
RMS Displacement 0.000101 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3 FREQ.LOG]]

<pre>
Low frequencies --- -32.4037 -32.3907 -11.4232 -0.0036 0.0075 0.0521
Low frequencies --- 1088.7639 1694.0249 1694.0253
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==
'''B3LYP/6-31G(d,p) level'''

[[File:Bh3nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000241 0.000450 YES
RMS Force 0.000053 0.000300 YES
Maximum Displacement 0.001381 0.001800 YES
RMS Displacement 0.000374 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL NH3BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2072 -0.0608 -0.0067 10.1080 16.5642 16.5733
Low frequencies --- 263.0162 631.3847 638.8686
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

== the association energy of NH<sub>3 </sub>BH<sub>3 </sub> Ammonia Boron==

E(NH3)= -56.558 a.u.
E(BH3)= -26.615 a.u.
E(NH3BH3)= -83.225 a.u.

association energy = E(NH3BH3)-[E(NH3)+E(BH3)] = 0.052 a.u. = 136.5 kJ/mol

Since BH3 always appears as B2H6 since it forms dative bonds with itself, I compared B-N association energy with B-H bond energy (389 kJ/mol). It can be said to be a weak bond since the difference is so that the bond could easily dissociate and return the structure B2H6.

== "heavy molecule" NI<sub>3 </sub>==
'''B3LYP/6-31G(d,p) level & psuedo-potentials'''

[[File:NI3 Summary.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000063 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000478 0.001800 YES
RMS Displacement 0.000273 0.001200 YES
</pre>

Frequency analysis log file [[Media:NI3 freq.log]]

<pre>
Low frequencies --- -12.7349 -12.7287 -6.2860 -0.0040 0.0188 0.0634
Low frequencies --- 101.0320 101.0328 147.4112
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3 freq.log</uploadedFileContents>
</jmolApplet></jmol>

optimised N-I distance is 2.18363 a.u.

== Ionic Liquids: Designer Solvents ==

'''[P(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''[N(CH3)4]+'''

[[File:Nh3 zyl.PNG|250px]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000287 0.000450 YES
RMS Force 0.000096 0.000300 YES
Maximum Displacement 0.001365 0.001800 YES
RMS Displacement 0.000678 0.001200 YES
</pre>

Frequency analysis log file [[Media:ZYL -N(CH3)4-+FREOUTPUT.LOG]]

<pre>
Low frequencies --- 0.0028 0.0031 0.0037 50.3282 50.3282 50.3282
Low frequencies --- 185.6971 210.7678 210.7678
</pre>

<jmol><script>frame 1.1</script><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ZYL -N(CH3)4-+FREOUTPUT.LOG</uploadedFileContents>
</jmolApplet></jmol>

File:ZYL -N(CH3)4-+FREOUTPUT.LOG

2019-05-09T15:03:54Z

Zl6217: