ChemWiki - User contributions [en]

Kk4717compy2inorg

2019-05-24T14:50:30Z

Kk4717: /* Molecular Orbitals */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|Wavenumber (cm-1) || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|93
|A"2
|Yes
|Out-of-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|2582
|0
|A'1
|no
|Totally symmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|600px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:49:59Z

Kk4717: /* Molecular Orbitals */

Kk4717compy2inorg

2019-05-24T14:49:38Z

Kk4717: /* Vibrational spectrum for BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|Wavenumber (cm-1) || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|93
|A"2
|Yes
|Out-of-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|2582
|0
|A'1
|no
|Totally symmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|600px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:48:58Z

Kk4717: /* Vibrational spectrum for BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A"2
|Yes
|Out-of-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|2582
|0
|A'1
|no
|Totally symmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|600px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:48:39Z

Kk4717: /* Vibrational spectrum for BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A''2
|Yes
|Out-of-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|1213
|14
|E'
|Very slight
|In-plane bend
|-
|2582
|0
|A'1
|no
|Totally symmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|-
|2716
|126
|E'
|Weak
|Asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|600px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:48:01Z

Kk4717: /* Vibrational spectrum for BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|Yes
|Out-of-plane bend
|-
|1213
|14
|E
|Very slight
|In-plane bend
|-
|1213
|14
|E
|Very slight
|In-plane bend
|-
|2582
|0
|A1
|no
|Totally symmetric stretch
|-
|2716
|126
|E
|Weak
|Asymmetric stretch
|-
|2716
|126
|E
|Weak
|Asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|600px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:47:52Z

Kk4717: /* Vibrational spectrum for BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|Yes
|Out-of-plane bend
|-
|1213
|14
|E
|Very slight
|In-plane bend
|-
|1213
|14
|E
|Very slight
|In-plane bend
|-
|2582
|0
|A1
|no
|Totally symmetric stretch
|-
|2716
|126
|E
|Weak
|Asymmetric stretch
|-
|2716
|126
|E
|Weak
|Asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|400px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:46:24Z

Kk4717: /* Vibrational spectrum for BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|400px|centre|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:42:25Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Fragment and Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) (Figure 10a) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) (Figure 10b) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) (Figure 10c) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because instead of radial nodes it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:36:44Z

Kk4717: /* Ionic liquids */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|600px|centre|thumb|frame|Figure 9. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T14:36:16Z

Kk4717: /* Ionic liquids */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted gives the calculation another degree of freedom that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|centre|thumb|frame|Figure 9. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO21.PNG|Figure 10a. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 10b. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 10c. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:47:32Z

Kk4717: /* NH3BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol). (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019).

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted means that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 9a. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 9b. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 9c. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 9d. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:45:23Z

Kk4717: /* NH3BH3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Chemistry Libretexts accessed: https://chem.libretexts.org/Courses/University_of_Missouri/MU%3A__1330H_(Keller)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds, 24.05.2019)

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted means that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 9a. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 9b. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 9c. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 9d. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:27:06Z

Kk4717: /* BI3 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== NI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| NI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted means that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 9a. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 9b. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 9c. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 9d. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:24:37Z

Kk4717: /* N(CH3)4 */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

For both N(CH3)4 and P(CH3)4 optimisation was done with unrestricted and restricted B3LYP/6-31G(d,p). Unrestricted means that the spins in the same orbital don't have to be degenerate often resulting in a lower optimised energy than with restricted. However this contradicts quantisation and is therefore physically impossible and therefore restricted is usually the preferred method for optimisation.

In this case the energies for both methods were the same, contrary to what was expected. Restricted method also gave slightly different low frequencies. Both optimisation results are given for both molecules.

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 9a. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 9b. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 9c. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 9d. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:04:28Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8a. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 8b. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 8c. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 8d. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 9a. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 9b. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 9c. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 9d. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:03:35Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|centre|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 9. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 10. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 11. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 14. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 15. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:03:13Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

[[File:KK4717_Charge_colour_range.PNG|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

<gallery mode=packed heights=200px>
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 9. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 10. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 11. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery mode=packed heights=200px>
File:KK4717_NCH34_MO_21_17_14.png|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 14. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 15. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:01:52Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

<gallery mode=packed heights=200px>
File:KK4717_Charge_colour_range.PNG|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 9. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 10. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 11. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery class="center">
File:KK4717_NCH34_MO_21_17_14.png|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 14. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 15. N[CH3]4 Molecular orbital 14.
</gallery>

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T10:00:59Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

'''Charges'''

<gallery class="center">
File:KK4717_Charge_colour_range.PNG|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 9. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 10. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 11. P[CH3]4 Charge graph with number representing the charge.
</gallery>

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

<gallery class="center">
File:KK4717_NCH34_MO_21_17_14.png|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14
File:KK4717_NCH34_MO21.PNG|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO).
File:KK4717_NCH34_MO17.PNG|Figure 14. N[CH3]4 Molecular orbital 17.
File:KK4717_NCH34_MO14.PNG|Figure 15. N[CH3]4 Molecular orbital 14.
</gallery>

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure 14. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure 15. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T09:59:28Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

<gallery class="center">
File:KK4717_Charge_colour_range.PNG|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4
File:KK4717_NCH34_Charge_Colour.PNG|Figure 8. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|Figure 9. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|Figure 10. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|Figure 11. P[CH3]4 Charge graph with number representing the charge.
</gallery>

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 8. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure 9. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 10. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure 11. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure 14. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure 15. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T09:58:37Z

Kk4717: /* Ionic liquids */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

<gallery class="center">
File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4
File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 8. N[CH3]4 Charge graph with colour representing the charge.
File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure 9. N[CH3]4 Charge graph with number representing the charge.
File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 10. P[CH3]4 Charge graph with colour representing the charge.
File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure 11. P[CH3]4 Charge graph with number representing the charge.
</gallery>

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 8. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure 9. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 10. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure 11. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure 14. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure 15. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T09:55:02Z

Kk4717:

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 8. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure 9. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 10. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure 11. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure 14. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure 15. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-24T09:53:21Z

Kk4717:

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG|bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 1. BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG|thumb|frame|Figure 2. BH3 calculated IR Spectra. ]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 3. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>Figure 4. NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>Figure 5. NH3BH3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>Figure 6. NI3 molecule. </title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

'''Unrestricted'''

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure 7. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 8. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure 9. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure 10. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure 11. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure 12. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure 13. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure 14. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure 15. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-23T18:27:10Z

Kk4717: /* Molecular Orbitals */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|centre|thumb|frame|Figure 5a. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-23T18:26:11Z

Kk4717: /* Molecular Orbitals */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|400px|thumb|frame|Figure 5a. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-23T18:25:58Z

Kk4717: /* Molecular Orbitals */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px|thumb|frame|Figure 5a. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-23T18:25:47Z

Kk4717: /* Molecular Orbitals */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px|thumb|right|frame|Figure 5a. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]]

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-23T18:23:58Z

Kk4717: /* Molecular Orbitals */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px|thumb|right|frame|Figure 5a. BH3 Molecular orbital diagram with real orbitals calculated using Gaussian. Diagram provided by Hunt, P., accessed http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf on 23.05.2019. ]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

Judging from the BH3 Molecular Diagram provided by Professor Hunt, the LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

Kk4717compy2inorg

2019-05-23T18:12:00Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO, molecular orbital 21 (E = -0.57934) of N[CH3]4 the five nodes cut through all carbon and the centran nitrogen atom increasing the overall energy of the molecule. However, the interactions in this molecular orbital are mainly mediated through molecule increasing the electron density in this molecule is along the bonds stabilising them. Overall the antibonding interactions reduces the bonding character and causes the orbital to be only weakly bonding. This orbital is also triply degenerate with molecular orbitals 19 and 20.

Molecular orbital 17 (E = -0.58034) is degenerate with orbitals 16 and 18. The strongest interactions in this orbital are between carbon p orbitals and two out of three hydrogens bonded to each of them. These are really close together and therefore cause strong stabilisation. Between the hydrogens that bond to the central carbon, there is a spacial antibonding character on the same plane as the carbon's bonding p orbital extending the node. There are also antibonding interactions between hydrogen s-orbitals of different phases bonded to different carbons. However, these interactions are weak as the distance between this destabilising interaction is high.

Molecular orbital 14 (E = -0.62247) is doubly degenerate with orbital 15. This orbital is different from the other two represented here because it has a two angular nodes centered around the nitrogen atom and cutting through the carbon atoms and N-C bonds. These destabilising interactions are countered by positive overlap between carbon p and hydrogen s orbitals. Opposite to MO 17, hydrogens in this molecular orbital have stabilising spacial interactions between protons bonded to different carbons. These are observed in three planes, the outer out-of-phase interactions being stronger than the middle in-phase one due to the relative distance between the same-phase hydrogens.

File:KK4717 NCH34 MO 21 17 14.png

2019-05-23T18:06:47Z

Kk4717: Kk4717 uploaded a new version of File:KK4717 NCH34 MO 21 17 14.png

File:KK4717 NCH34 MO 21 17 14.png

2019-05-23T17:52:57Z

Kk4717: Kk4717 uploaded a new version of File:KK4717 NCH34 MO 21 17 14.png

Kk4717compy2inorg

2019-05-23T17:15:39Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]
[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO of N[CH3]4

Kk4717compy2inorg

2019-05-23T17:14:48Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

[[File:KK4717_NCH34_MO21.PNG|200px|thumb|left|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|centre|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|right|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO of N[CH3]4

Kk4717compy2inorg

2019-05-23T17:13:50Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

In the HOMO of N[CH3]4

Kk4717compy2inorg

2019-05-23T16:45:39Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

Kk4717compy2inorg

2019-05-23T16:45:19Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

'''Charges'''

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

[[File:KK4717_NCH34_MO21.png|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

Kk4717compy2inorg

2019-05-23T16:44:37Z

Kk4717: /* Charges and MOs */

== Year 2 Inorganic computational lab ==

=== BH3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_BH3_FREQ.LOG| bh3_frequency.log]]

<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

[[File:kk4717_BH3_Summary.PNG]]

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Vibrational spectrum for BH3====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|1213
|14
|E
|very slight
|in-plane bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|-
|2716
|126
|E
|weak
|asymmetric stretch
|}

[[File:KK4717_BH3_IR_SPECTRA.PNG]]

On the IR spectrum of BH3, only three peaks are observed. This is because out of the six vibrations only five cause a change in dipole and are therefore IR active. The sixth, at 2582 cm-1, is symmetrical and non IR active.

From the five visible peaks two pairs have the same vibrational energy and therefore also vibrate at the same frequency. This results in only observing three distinctive peaks on the IR spectrum: one stretch and two bends.

==== Molecular Orbitals ====

[[File:KK4717_BH3_MO_DIAGRAM_REAL.png|700px]]

REFERENCE HUNT TUTORIAL BH3 MO GRAPH

The LCAO MOs give a rough representation of the real MOs, but it doesn't predict the shapes correctly. The real molecular orbital shapes are different from those LCAO predicts due to interactions between the atomic orbitals.

Using LCAO as a tool is very useful but one needs to be especially cautious when representing higher molecular orbitals that have complex interactions between the atomic orbitals.

=== NH3BH3 ===

'''NH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3_FREQ2.LOG| nh3_frequency.log]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

[[File:KK4717_NH3_Summary.PNG]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

'''NH3BH3'''
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000044 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000405 0.001800 YES
RMS Displacement 0.000129 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NH3BH3_FREQ2.LOG| nh3bh3_frequency.log]]

<pre>
Low frequencies --- -0.1066 -0.0697 -0.0073 15.5156 15.5300 19.3320
Low frequencies --- 263.8240 632.6555 639.3404
</pre>

[[File:KK4717_NH3BH3_Summary2.PNG]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NH3BH3_FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
| Species || Energy (AU) || Energy (kJ/mol)
|-
|E(BH3)
| -26.61532
|
|-
|E(NH3)
| -56.55777
|
|-
|E(NH3BH3)
| -83.22469
|
|-
|ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
| -0.0516
| -135
|}

The N-B bond strength (-135 kJ/mol) is relatively weak compared to other covalent bonds like N-C (305 kJ/mol) or N-N (167 kJ/mol) (Reference: https://chem.libretexts.org/Bookshelves/General_Chemistry/Map%3A_Chemistry_-_The_Central_Science_(Brown_et_al.)/08._Basic_Concepts_of_Chemical_Bonding/8.8%3A_Strength_of_Covalent_Bonds)

=== BI3 ===

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000028 0.001200 YES
</pre>

B3LYP/6-31G(d,p)LANL2DZ NI3

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000459 0.001800 YES
RMS Displacement 0.000285 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NI3_FREQ_GEN_FINISHED.log| BI3_frequency.log]]

<pre>
Low frequencies --- -5.5587 -5.4901 0.0002 0.0003 0.0004 6.5130
Low frequencies --- 101.1565 101.2827 148.4562
</pre>

[[File:KK4717_NI3_Summary.PNG]]

Optimised N-I distance is 2.184 Å.

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>KK4717_NI3_FREQ_GEN_FINISHED.log</uploadedFileContents>
</jmolApplet></jmol>

=== Ionic liquids ===

==== N(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000043 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G.LOG| NCH34_frequency.log]]

<pre>
Low frequencies --- 0.0006 0.0010 0.0011 34.8378 34.8378 34.8378
Low frequencies --- 217.4637 316.5664 316.5664
</pre>

[[File:KK4717_NCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000046 0.001800 YES
RMS Displacement 0.000023 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_NCH34_FREQ_631G_R2.LOG| NCH34_frequency_restricted.log]]

<pre>
Low frequencies --- -0.0014 -0.0014 -0.0013 21.9732 21.9732 21.9732
Low frequencies --- 189.1931 293.0643 293.0643
</pre>

[[File:KK4717_NCH34_Summary2_R.PNG]]

==== P(CH3)4 ====

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000234 0.001800 YES
RMS Displacement 0.000144 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0019 -0.0016 -0.0016 50.3137 50.3137 50.3137
Low frequencies --- 185.6718 210.7297 210.7297
</pre>

[[File:KK4717_PCH34_Summary2.PNG]]

'''Restricted'''

B3LYP/6-31G(d,p) Restricted

<pre>
Item Value Threshold Converged?
Maximum Force 0.000045 0.000450 YES
RMS Force 0.000013 0.000300 YES
Maximum Displacement 0.000230 0.001800 YES
RMS Displacement 0.000141 0.001200 YES
</pre>

Frequency file: [[Media:KK4717_PCH34_FREQ_631G_R.LOG| PCH34_frequency.log]]

<pre>
Low frequencies --- -0.0021 0.0014 0.0019 24.1090 24.1090 24.1090
Low frequencies --- 159.8024 194.6110 194.6110
</pre>

[[File:KK4717_PCH34_Summary2_R.PNG]]

==== Charges and MOs ====

[[File:KK4717_Charge_colour_range.PNG|200px|thumb|frame|Figure X. Colour range showing the charge of N[CH3]4 and P[CH3]4]]

[[File:KK4717_NCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with colour representing the charge.]]
[[File:KK4717_NCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. N[CH3]4 Charge graph with number representing the charge.]]
[[File:KK4717_PCH34_Charge_Colour.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with colour representing the charge. ]]
[[File:KK4717_PCH34_Charge_Value.PNG|200px|thumb|frame|Figure X. P[CH3]4 Charge graph with number representing the charge.]]

{| class="wikitable"
|+
|-
| Species || Central Atom (N or P) || Carbon || Hydrogen
|-
|N(CH3)4
| -0.295
| -0.483
| 0.269
|-
|P(CH3)4
| 1.667
| -1.060
| 0.298
|}

Even though formally nitrogen atom in N[CH3]4 has a positive charge, in reality it is slightly negatively charged. Nitrogen is more electronegative than carbon and therefore it pulls electron density away from carbon making the carbon less negatively charged as well. This is due to nitrogen having more protons and the same number of orbitals as carbon. The positive charge on this molecule is located on the low electronegative hydrogens.

With P[CH3]4, the negative charge on carbon is higher than that of in N[CH3]4. This is because phosphorous, even though having higher number of protons in the nucleus, has a lower electronegativity due to extra orbitals 3s and 3p. In this case, carbon with higher electronegativity pulls electrons away from phosphorous atom making it positively charged. Carbon itself is negatively charged due to that.

'''Molecular Orbitals'''

[[File:KK4717_NCH34_MO_21_17_14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital diagrams of orbitals 21 (HOMO), 17 and 14]]

[[File:KK4717_NCH34_MO21.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 21 (HOMO). ]]
[[File:KK4717_NCH34_MO17.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 17. ]]
[[File:KK4717_NCH34_MO14.PNG|200px|thumb|frame|Figure X. N[CH3]4 Molecular orbital 14. ]]

File:KK4717 NCH34 MO14.PNG

2019-05-23T16:31:57Z

Kk4717:

File:KK4717 NCH34 MO17.PNG

2019-05-23T16:31:48Z

Kk4717:

File:KK4717 NCH34 MO21.PNG

2019-05-23T16:31:40Z

Kk4717:

File:KK4717 NCH34 MO 21 17 14.png

2019-05-23T16:31:19Z

Kk4717:

Kk4717compy2inorg

2019-05-23T14:04:56Z

Kk4717: /* Charges and MOs */

File:KK4717 Charge colour range.PNG

2019-05-23T13:48:23Z

Kk4717:

Kk4717compy2inorg

2019-05-23T13:48:07Z

Kk4717: /* Charges and MOs */

Kk4717compy2inorg

2019-05-23T13:46:00Z

Kk4717: /* Charges and MOs */

Kk4717compy2inorg

2019-05-23T13:40:49Z

Kk4717: /* Ionic liquids */

File:KK4717 NCH34 Charge Colour.PNG

2019-05-23T13:39:59Z

Kk4717:

File:KK4717 PCH34 Charge Colour.PNG

2019-05-23T13:39:47Z

Kk4717:

File:KK4717 NCH34 Charge Value.PNG

2019-05-23T13:39:38Z

Kk4717: