ChemWiki - User contributions [en]

Rep:Mod:inorganicjp2517

2019-05-23T14:58:24Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|-
|Δ charge||0.591
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|-
|Δ charge||2.727
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its spherical symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital due to it being spherically symmetric, however the difference here is the amount of antibonding character, leading to a different molecule MO.

[[File:Jp2517LCAOMO21.PNG]][[File:Jp2517LCAOMO21b.PNG]]

Molecular Orbital 21 is the HOMO and features a mixture of bonding and antibonding interactions. The ligand FOs have similar symmetry to a p-orbital, given that there are nodes halfway across the C-H bonds, thus can be approximated as such.

====Final Note====
The thing I found most useful about this project was being able to see the concepts we've studied in Dr. Hunt's Molecular Orbital Theory course being brought to life in a computational chemistry environment. Having studied BH3 on paper, it was fascinating to optimise it and play around with the real MOs. The larger molecules, such as [N(CH3)4]+, have some fantastically complicated Molecular Orbitals. I feel that I've been able to use this lab to brush up on my knowledge of Molecular Orbital theory and apply some of the concepts we've learned to their real-world applications.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:58:08Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|-
|Δ charge||5.91
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|-
|Δ charge||2.727
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its spherical symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital due to it being spherically symmetric, however the difference here is the amount of antibonding character, leading to a different molecule MO.

[[File:Jp2517LCAOMO21.PNG]][[File:Jp2517LCAOMO21b.PNG]]

Molecular Orbital 21 is the HOMO and features a mixture of bonding and antibonding interactions. The ligand FOs have similar symmetry to a p-orbital, given that there are nodes halfway across the C-H bonds, thus can be approximated as such.

====Final Note====
The thing I found most useful about this project was being able to see the concepts we've studied in Dr. Hunt's Molecular Orbital Theory course being brought to life in a computational chemistry environment. Having studied BH3 on paper, it was fascinating to optimise it and play around with the real MOs. The larger molecules, such as [N(CH3)4]+, have some fantastically complicated Molecular Orbitals. I feel that I've been able to use this lab to brush up on my knowledge of Molecular Orbital theory and apply some of the concepts we've learned to their real-world applications.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:49:40Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its spherical symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital due to it being spherically symmetric, however the difference here is the amount of antibonding character, leading to a different molecule MO.

[[File:Jp2517LCAOMO21.PNG]][[File:Jp2517LCAOMO21b.PNG]]

Molecular Orbital 21 is the HOMO and features a mixture of bonding and antibonding interactions. The ligand FOs have similar symmetry to a p-orbital, given that there are nodes halfway across the C-H bonds, thus can be approximated as such.

====Final Note====
The thing I found most useful about this project was being able to see the concepts we've studied in Dr. Hunt's Molecular Orbital Theory course being brought to life in a computational chemistry environment. Having studied BH3 on paper, it was fascinating to optimise it and play around with the real MOs. The larger molecules, such as [N(CH3)4]+, have some fantastically complicated Molecular Orbitals. I feel that I've been able to use this lab to brush up on my knowledge of Molecular Orbital theory and apply some of the concepts we've learned to their real-world applications.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:48:35Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

[[File:Jp2517LCAOMO21.PNG]][[File:Jp2517LCAOMO21b.PNG]]

Molecular Orbital 21 is the HOMO and features a mixture of bonding and antibonding interactions. The ligand FOs have similar symmetry to a p-orbital, given that there are nodes halfway across the C-H bonds, thus can be approximated as such.

====Final Note====
The thing I found most useful about this project was being able to see the concepts we've studied in Dr. Hunt's Molecular Orbital Theory course being brought to life in a computational chemistry environment. Having studied BH3 on paper, it was fascinating to optimise it and play around with the real MOs. The larger molecules, such as [N(CH3)4]+, have some fantastically complicated Molecular Orbitals. I feel that I've been able to use this lab to brush up on my knowledge of Molecular Orbital theory and apply some of the concepts we've learned to their real-world applications.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:43:40Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

[[File:Jp2517LCAOMO21.PNG]][[File:Jp2517LCAOMO21b.PNG]]

Molecular Orbital 21 is the HOMO and features a mixture of bonding and antibonding interactions. The ligand FOs have similar symmetry to a p-orbital, given that there are nodes halfway across the C-H bonds, thus can be approximated as such.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

File:Jp2517LCAOMO21b.PNG

2019-05-23T14:41:13Z

Jp2517:

File:Jp2517LCAOMO21.PNG

2019-05-23T14:40:50Z

Jp2517:

Rep:Mod:inorganicjp2517

2019-05-23T14:13:59Z

Jp2517: /* Heavy Molecule Optimisation */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:13:42Z

Jp2517: /* Energy Calculation */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1 [2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:13:32Z

Jp2517: /* Energy Calculation */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1[2] . However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:13:14Z

Jp2517: /* Energy Calculation */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 [2] and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T14:08:32Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. Similarly to MO 6, the Ligand FO can be approximated to an s-orbital, however the difference here is the amount of antibonding character, leading to a different molecule MO.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

File:Jp2517LCAOMO10.PNG

2019-05-23T14:06:46Z

Jp2517: Jp2517 uploaded a new version of File:Jp2517LCAOMO10.PNG

Rep:Mod:inorganicjp2517

2019-05-23T14:04:59Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and the ligand FO can be approximated to an s-orbital for simplification due to its symmetry.

[[File:Jp2517LCAOMO10.PNG]]

Molecular Orbital 10 is a valence antibonding orbital. The

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

File:Jp2517LCAOMO10.PNG

2019-05-23T14:04:01Z

Jp2517:

Rep:Mod:inorganicjp2517

2019-05-23T14:02:48Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly bonding character, hence why it appears red, and can be approximated to an s-orbital for simplification due to its symmetry.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:56:22Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

Molecular Orbital 6 is a valence bonding orbital deep in energy with mostly antibonding character, hence why it appears red, and can be approximated to an s-orbital for simplification due to its symmetry.

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:54:56Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

[[File:Jp2517LCAOMO6.PNG]]

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

File:Jp2517LCAOMO6.PNG

2019-05-23T13:54:36Z

Jp2517:

Rep:Mod:inorganicjp2517

2019-05-23T13:39:29Z

Jp2517: /* [N(CH3)4]+ */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them.

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

From left to right, the MOs in question are MO 6, MO 10 and MO 21 (the HOMO).

===LCAO Diagrams===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:38:55Z

Jp2517: /* LCAO Diagrams */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them

===LCAO Diagrams===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:38:27Z

Jp2517: /* LCAO Diagram */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them

===LCAO Diagrams===

[[File:Jp2517Nr4mo6.PNG]][[File:Jp2517Nr4mo10.PNG]][[File:Jp2517Nr4mo21.PNG]]

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

File:Jp2517Nr4mo21.PNG

2019-05-23T13:37:31Z

Jp2517:

File:Jp2517Nr4mo10.PNG

2019-05-23T13:37:02Z

Jp2517:

File:Jp2517Nr4mo6.PNG

2019-05-23T13:36:39Z

Jp2517:

Rep:Mod:inorganicjp2517

2019-05-23T13:32:23Z

Jp2517: /* [N(CH3)4]+ */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
All of the occupied MOs for [N(CH3)4]+ were visualised, including the five lowest-energy unoccupied Molecular Orbitals, making 26 in total. Three of these were chosen and the LCAO diagram was generated for them

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:25:19Z

Jp2517: /* MO Diagram */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. The 'real' MOs have been blended together a bit more, with continuous regions of each phase, unlike on the LCAO diagram, where orbitals of the same phase are not necessarily shown to overlap. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:22:58Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:20:33Z

Jp2517: /* Ionic Liquids */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:19:53Z

Jp2517: /* [P(CH3)4]+ */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:19:32Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:18:56Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

[N(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||+0.269
|}

[P(CH3)4]+
{| class="wikitable"
|+
|-
|Atom||Charge
|-
|P||+1.667
|-
|C||-1.060
|-
|H||+0.298
|}
The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:17:27Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

{| class="wikitable"
|+
|-
|Atom||Charge
|-
|N||-0.295
|-
|C||-0.483
|-
|H||0.269
|}

The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T13:14:18Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T12:39:33Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

Based on the results for [N(CH3)4]+, it's clear that the traditional description, featuring a +1 charge on the Nitrogen, is largely inaccurate. This traditional description represents a +1 charge seated wholly on the Nitrogen, with the other atoms being neutral, which is more of a valence-bond approach. By computing the Molecular Orbitals and producing the charge distribution for [N(CH3)4]+, we can see that the charge is in fact spread more evenly across all the atoms in the molecule, and is specifically located primarily on the Hydrogen atoms in this cation.

Conversely, in [P(CH3)4]+, the traditional description is more accurate, with most of the positive charge residing on the central P atom.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T12:31:35Z

Jp2517: /* Charge Distribution Comparison */

=BH3=
==Lower Basis Set==
Computational Level: B3LYP

Basis Set: 3-21G

[[File:jp2517Bh3summary321g.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000692 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

</pre>

Log file: [[Media:JP2517 BH3 OPT321.LOG| JP2517 BH3 OPT321.LOG]]

==Higher Basis Set==
Computational Level: B3LYP

Basis Set: 6-31G(d.p)

[[File:jp2517Bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000849 0.001800 YES
RMS Displacement 0.000415 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3 OPT.LOG| JP2517 BH3 OPT.LOG]]

==Frequency Calculation==
Method: Frequency

Computational Level: B3LYP

Basis Set: 6-31G(d.p)

It's worth noting that before the frequency analysis was performed, the molecule was constrained manually to D3h symmetry and reoptimised.

[[File:jp2517Bh3frequencysummary.PNG]]

Frequency file: [[Media:JP2517 BH3 FREQ.LOG| JP2517 BH3 FREQ.LOG]]

<pre>
Low frequencies --- -0.2279 -0.0081 -0.0012 22.0037 22.0049 24.0346
Low frequencies --- 1163.1731 1213.2725 1213.2727
</pre>

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

{| class="wikitable"
|+
|-
|Wavenumber (cm-1)||Intensity (arbitrary units)||Symmetry||IR Active?||type
|-
|1163||92||A2''||Yes||In-plane symmetric bend
|-
|1213||14||E''||Yes||Out-of-plane asymmetric bend
|-
|1213||14||E''||Yes||Out-of-plane symmetric bend
|-
|2582||0||A1'||No||Symmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|2715||126||E'||Yes||Asymmetric stretch
|-
|}

[[File:jp2517Bh3ir.PNG|500px]]

The IR spectrum shows only three peaks, despite there being six modes present. The one occurring at 2582 cm-1 is IR inactive, as the symmetry with which the stretch occurs results in no change in dipole moment. There are two more pairs of vibrations which occur at the same wavenumber, 1213 cm-1 and 2715 cm-1, which overlap, meaning only three peaks are left in the spectrum. The peaks occurring at 1213 cm-1 involve only a slight change in dipole moment, thus less IR radiation is absorbed in the vibration, hence why they appear with less intensity on the spectrum.

==MO Diagram==
[[File:jp2517Bh3modiagram.PNG|500px]]

[1] Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

As can be seen on the diagram, there aren't really any significant differences between the real MOs and the LCAO MOs in terms of their shape and relative energy levels, which is a good indicator of the usefulness of qualitative MO Theory. From here, it can be used to predict the reactivity of the molecule based on which MOs are occupied.

==Association Energies==
We already have the energy of BH3, and it's -26.62 a.u.

Therefore, to compute the reaction energy, we need the energies of the optimised NH3BH3 molecule and the NH3 molecule.

==NH3BH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3bh3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000539 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

Log file: [[Media:JP2517 BH3NH3 OPTAGAIN2.LOG|JP2517 BH3NH3 OPTAGAIN2.LOG]]

<pre>
Low frequencies --- -0.0250 -0.0031 0.0012 17.1394 17.1417 37.1989
Low frequencies --- 265.8013 632.2135 639.3553
</pre>

Frequency File: [[Media:JP2517 BH3NH3 FREQ2.LOG|JP2517 BH3NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 BH3NH3 FREQ2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3 Optimisation and Frequency Analysis==
Computational Level: B3LYP

Basis Set: 6-31G (d.p.)

[[File:Jp2517Nh3summary.PNG]]

<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>

Log file: [[Media:JP2517 NH3 OPT.LOG|JP2517 NH3 OPT.LOG]]

<pre>
Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368
</pre>

Frequency file: [[Media:JP2517 NH3 FREQ2.LOG|JP2517 NH3 FREQ2.LOG]]

<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NH3 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy Calculation==
From this it can be seen that the energies of the molecules are as follows:

E(NH3)= -56.56 a.u.

E(BH3)=-26.62 a.u.

E(NH3BH3)= -83.22 a.u.

Therefore, ΔE for this process = E(NH3BH3)-[E(NH3)+E(BH3)] = -0.04 a.u.

Converted to kJmol-1, this is -105.02 kJmol-1

Based on this calculation, it's clear that the B-N dative bond is pretty weak, when compared to a B-B bond at 293 kJmol-1 and an N-N bond at 167 kJmol-1. However, this process is overall exothermic, thus there is energy gain in forming it.

=Heavy Molecule Optimisation=
NI3 is the molecule to be optimised.

Method: B3LYP

Basis Set: GEN

[[File:Jp2517Ni3summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000084 0.000450 YES
RMS Force 0.000062 0.000300 YES
Maximum Displacement 0.001108 0.001800 YES
RMS Displacement 0.000520 0.001200 YES
</pre>

Log file: [[Media:JP2517 NI3 OPT2.LOG|JP2517 NI3 OPT2.LOG]]

<pre>
Low frequencies --- -1.7762 -1.7378 -0.7557 -0.0031 0.0322 0.0731
Low frequencies --- 101.3565 101.3572 148.4310
</pre>

Frequency file: [[Media:JP2517 NI3 FREQ.LOG|JP2517 NI3 FREQ.LOG]]

<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NI3 OPT2.LOG</uploadedFileContents>
</jmolApplet></jmol>

NOTE TO SELF: DEPOSIT FINAL OPTIMISED FILE TO DSPACE?

From the calculations, we can see that the optimised N-I distance is 2.18 Å, much longer than the N-H distance in NH3 due to the larger and more diffuse Iodine orbitals providing reduced overlap with the N orbitals, hence the longer, weaker bond.

=Ionic Liquids=
Two ionic liquids will be investigated: [N(CH3)4]+ and [P(CH3)4]+, in order to investigate their charge distributions and molecular orbitals, with a view to predicting their properties without synthesising them.

==[N(CH3)4]+==
===Optimisation===

Before commencing optimisation, the molecule was constrained to Td symmetry.

Method: B3LYP

Basis Set: 6-31G(d,p)

[[File:Jp2517Nr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000027 0.000300 YES
Maximum Displacement 0.000151 0.001800 YES
RMS Displacement 0.000067 0.001200 YES
</pre>

Log file: [[Media:JP2517 NR4 OPT.LOG|JP2517 NR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0005 -0.0004 0.0003 22.7128 22.7128 22.7128
Low frequencies --- 190.7454 294.0627 294.0627
</pre>

Frequency file: [[Media:JP2517 NR4 FREQ.LOG|JP2517 NR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 NR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==[P(CH3)4]+==

===Optimisation===

[[File:Pr4summary.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000030 0.000450 YES
RMS Force 0.000012 0.000300 YES
Maximum Displacement 0.000107 0.001800 YES
RMS Displacement 0.000044 0.001200 YES
</pre>

Log file: [[Media:JP2517 PR4 OPT.LOG|JP2517 PR4 OPT.LOG]]

<pre>
Low frequencies --- -0.0016 0.0019 0.0020 25.3058 25.3058 25.3058
Low frequencies --- 161.2513 195.7468 195.7468
</pre>

Frequency file: [[Media:JP2517 PR4 FREQ.LOG|JP2517 PR4 FREQ.LOG]]

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>JP2517 PR4 OPT.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge Distribution Comparison==
The Charge Distribution was computed for both molecules and yielded the following images.

[[File:Nr4chargedist.PNG|thumb|none|[N(CH3)4]+]][[File:Jp2517Pr4chargedist.PNG|thumb|none|[P(CH3)4]+]]

The differences between the two charge distributions are as follows:
*The amount of charge residing on the central atom; Nitrogen in [N(CH3)4]+ carries much more electron density (-0.295) than Phosphorus in [P(CH3)4]+ (+1.667). This is largely due to the higher electronegativity of N compared to P. Nitrogen has smaller orbitals (in fact, a lack of d-orbitals), meaning the effective nuclear charge on the outermost electrons is greater, hence its ability to attract a negative charge is greater, which is why more negative charge resides on it in this complex.
*The polarity of the P/N atom to Carbon bond; [N(CH3)4]+ ranges from -0.483 to +0.269, while [P(CH3)4]+ ranges from -1.060 to +1.667, meaning its bonds are more polar overall. This is due to the fact that while Nitrogen is more electronegative than Phosphorus, Nitrogen has a more similar electronegativity to Carbon than Phosphorus, thus the polarity of the Group 5 element to C bond is lower for Nitrogen.
*The amount of electron density residing on H; for [N(CH3)4]+ the relative charge distribution on the H atoms is +0.269, while for [P(CH3)4]+ the Hydrogens have less electron density on them, at +0.298. This is due to the fact that in [N(CH3)4]+, the carbons of the methyl groups carry less of the electron density (-0.483) than in the methyl groups of [P(CH3)4]+ (-1.060), therefore there is less electron density shared among the Hydrogens in [P(CH3)4]+, which is why they're sharing more positive charge.

==Molecular Orbitals==
===[N(CH3)4]+===
3 valence MOs

===LCAO Diagram===

=References=
1. Diagram adapted from: Dr Patricia Hunt, BH3 MO Diagram, http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

2. http://www.wiredchemist.com/chemistry/data/bond_energies_lengths.html

Rep:Mod:inorganicjp2517

2019-05-23T12:18:25Z

Jp2517: /* Charge Distribution Comparison */

Rep:Mod:inorganicjp2517

2019-05-23T11:00:27Z

Jp2517: /* Charge Distribution Comparison */

Title=Mod:inorganic wiki page instructions

2019-05-23T10:58:17Z

Jp2517: /* Thumbs and captions */

=‘How to create a wiki’ wiki=

This page should provide you with all the necessary information required to put together a wiki page.

=Getting started=

Start up firefox
goto the URL '''www.ch.ic.ac.uk''', this will default to https://wiki.ch.ic.ac.uk/wiki/index.php?title=Main_Page

You should see something like this: [[image:wiki_start.jpg|thumb|center|400px|caption]]

You need to login to your imperial college account before you can make changes to the wiki (login by clicking on the link outlined in red)

Once logged in to generate a page you only have to define it! So in the URL box delete just the current page's title and then add in your own

for example ''' title=Mod:XYZ1234'''

where the Mod indicates this is a report associated with the modelling course, and XYZ1234 is your secret password for the report.

Make sure you choose something unique! Remember there are approximately 160 other people also doing a wiki, and that is just this year's students!

You should end up with a wiki page with a url of the following form

wiki.ch.ic.ac.uk/wiki/index.php?title=Mod:XYZ1234

(do not copy and paste the link above as some people have been getting an error when they do this)

It should tell you there is no text in this page. If an already existing page comes up, just try another more unique password. Here I used the title Mod:Ttestpage
[[image:wiki_blank.jpg|thumb|center|400px|caption]]

You should now click on the "edit this page"or the "create source" link to start, see the red box on the image above.
[[image:wiki_test_page.jpg|thumb|center|400px|caption]]

=Sections, headings and table of contents=

Sections and subsections are introduced by headings. These headings help to break up text, organise content, and populate the table of contents.

{| class="wikitable"
! Description
! What you type
! What it looks like
|-
|''Heading Formatting''
|
<tt><nowiki>== Section Title ==</nowiki></tt> 
<tt><nowiki>=== Subtitle ===</nowiki></tt> 
<tt><nowiki>==== Sub-subtitle ====</nowiki></tt> 
|
<div style="font-size:150%;padding-bottom:0.17em;padding-top:0.5em;margin-bottom:0.6em;border-bottom:1px solid rgb(170,170,170);">Section title</div>
<div style="font-size:132%;font-weight:bold;padding-bottom:0.17em;padding-top:0.5em;margin-bottom:0.3em;">Subtitle</div>
<div style="font-size:116%;font-weight:bold;padding-bottom:0.17em;padding-top:0.5em;margin-bottom:0.3em;">Sub-subtitle</div>
|}

Your page should be divided into sections, using the section heading syntax above. For each page with more than three section headings, a table of contents (TOC) is automatically generated which will make navigating your page easier.

=Subscripts, superscripts and styles=

In the table below you will find a list of the most common formatting styles which you will need to use in your own wiki page:

{| class="wikitable"
! Description
! What you type
! What it looks like
|-
|rowspan=5|''Formatting''
|-
|<pre>bold or '''bold'''</pre>
|style="text-align: center;"|bold
|-
|<pre>italic or ''italic''</pre>
|style="text-align: center;"|italic
|-
|<pre>underline</pre>
|style="text-align: center;"|underline
|-
|<pre>bold and italic or '''''bold & italic''''' </pre>
|style="text-align: center;"|bold and italic
|-
|''Subscripts''
|<pre>x1 x2 x3 </pre>
|x1 x2 x3
|-
|''Superscripts''
|<pre>x1 x2 x3 </pre>
|x1 x2 x3
|-
| colspan="3"|You can also format titles:
|-
|''Heading Formatting''
|<pre>===Subtitle===</pre>
|

<div style="font-size:132%;font-weight:bold;padding-bottom:0.17em;padding-top:0.5em;margin-bottom:0.3em;">Subtitle</div>
|}

It does not matter which code you use to format your text although stick with one style and use it throughout in order to avoid confusion.

=Links=

To add a link give the URL within a set of square brackets, the displayed link goes after a "vertical bar" as follows:

<nowiki>[[name of page| text to display]]</nowiki>

For more detailed instructions for your wiki writing go to the [[Mod:writeup|comp chem lab]] page.

If you want to add a DOI link [https://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/0d_publishing_Dspace.html click].

=Uploading files=

The first step in using an image or other file is to upload it to the suitably named “Upload file” page. You can reach this page by clicking the link on the left hand side of your wiki page as illustrated below.

[[File:Upload_file_link.png|center|none|100px]]

Select the file you wish to upload by clicking browse and navigating to the location of the file.

[[File: Upload_page_browse.png|center|750px]]

Scroll to the bottom of the Upload page and click upload file.

==Important!==

You must upload your finished .log files, and link to them on your wiki. The .log file will then also be used to create a moving jmol image. How to do these will be explained below.

If you upload a file with the same name as a previously uploaded file that file will be lost! '''So please name your files including your username''', for example: rr1210_nh3.log.

==Embedding an image on your wiki==

Once you have uploaded a file, you can incorporate it into your wiki page by selecting the picture button ([[File: Wiki_picture_button_image.png]]) in the wiki toolbar.

This will add the following text:

<pre>[[File:]]</pre>

In order to embed your image into the wiki page simply write the name of the file after the colon. For example:

<pre>[[File:Benzene_3D.png]]</pre>

will appear as shown below on your wiki page.

[[File:Benzene_3D.png|250px]]

==Resizing images==

Sometimes when you embed an image you have uploaded, such as a Gaussview picture or a screenshot you have taken, the image can be rather large. You can manipulate the image size displayed on screen by adding a pipe (vertical bar) after the picture file extention then a number followed by px:

<pre>[[File:Benzene_3D.png|150px]]</pre>

The number dictates the width of the image and 'px' stands for pixels therefore the image would as follows:

[[File:Benzene_3D.png|150px]]

This technique is particularly useful if you want to embed images in a table.

==Thumbs and captions==

Some images may be too large for your wiki page but the clarity may be poor when resized. Pictures such as MO diagrams may be too large (in dimension and file size) to embed directly on your page as they would result in slow loading. Instead you can add a thumbnail of the image along with a caption describing the picture which will link to the upload file. To do this you need to add a pipe followed by the word thumb (for thumbnail) followed by another pipe and the corresponding caption text terminated with a full stop. See below for an example

<pre>[[File:Benzene_3D.png|thumb|A Gaussview image of an optimised benzene molecule.]]</pre>

The image will appear on your wiki page as follows:

[[File:Benzene_3D.png|thumb|none|A Gaussview image of an optimised benzene molecule.]]

Clicking the thumb nail will take you to the uploaded file page for the image.

==Repositioning images==

The default position for an embedded image is to the left hand side of the wiki page however if you would prefer to center the graphic then add a pipe and the text center after the file name.

<pre>[[File:Benzene_3D.png|thumb|center|A Gaussview image of an optimised benzene molecule.]]</pre>

This will appear as follows on your wiki page:

[[File:Benzene_3D.png|thumb|center|none|A Gaussview image of an optimised benzene molecule.]]

You can search the web for [https://www.mediawiki.org/wiki/Help:Images more options on how to format images] in a wiki.

=Adding Jmol files of your molecule=

==create your file==
First years: Upload your .log file as explained above for image files. Now you can continue to the [[#How to add the jmol to your wiki|How to add the jmol to your wiki]] section.

Later years: If you have run a large job, then there are two options to avoid uploading the large .log file directly to the wiki.
One is to use gaussview to save a copy of your molecule as a .mol file or to make a .xyz file.

==upload your file==
Now upload your file to the wiki

Go to your wiki-page, click on "upload file" in the column on the left

follow the local instructions

copy the file-name generated into the script below

==How to add the jmol to your wiki==
You can have the jmol embedded directly into your wiki page, please don't do this more than 5 times on one page as it may become slow to load.

:add the following text to your wiki page replacing "username_molecule_1.log" with your file name.

<pre><jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>username_molecule_1.log</uploadedFileContents>
</jmolApplet></jmol></pre>

::this will produce the following:
<jmol><jmolApplet>
<title>test molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Bh3_631gdp opt.mol</uploadedFileContents>
</jmolApplet></jmol>
:::the title tag is self explanatory
:::the colour tag sets the background colour to black
:::the size tag sets the size of the jmol image to display
:::the uploadfile tag determines the file to load

'''Note:''' log files from optimizations will show by default the starting un-optimized structure. You can right-click on the JSmol applet and under the menu item "model" you will find all the structures present in the file. To make the optimize structure be the one show when the wiki is opened, you should add to the code above, somewhere between the tags <jmolApplet> and </jmaolApplet>, a line with:
<pre>
<script>frame x.y</script>
</pre>
where x.y are the numbers defining the frame of the optimized structure.

More complex jmol activities such as adding vibrations and MOs can be found here:[[Mod:writeup#Advanced JSmol|advanced jmol]]

'''Beware!''' You can corrupt your wiki by not putting the correct XML for the jmol in, recovering from such errors is difficult! Save your wiki before inserting any jmol molecules, and be careful that you put in the text exactly as it is here.

There is a common error when inserting a Jmol image. Using the above method a black box will appear with red writing within it. Shown below.

[[File:Jmol error.png]]

The error occurs because the file is not on the system. The file not being on the system is either because is has not been uploaded, or the file name is different.

'''Beware!''' underscores often become spaces so check carefully as your file name might well have changed!

The file name "klw14_molecule.log" will become "klw14 molecule.log" once uploaded to the wiki.

You can check you have uploaded the file or check the file name of your upload by clicking on the LIST OF UPLOADED FILES link at the top of the upload home page and search the uploaded files using your username.

===using a mol file===
::open your molecule in gaussview
::choose save
::in the options choose save as a mol file
::here is what gaussview saved for my file:
<pre>
Title Card Required

Created by GaussView 4.1.2
4 3 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 1.1945 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1.0345 -0.5973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0345 -0.5973 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
1 4 1 0 0 0 0
</pre>

===making an xyz file===
:: you need to make this file yourself in a text editor, this file has 3 sections
:::#first line: number of atoms in the molecule
:::#second line: comments or title
:::#following lines: atomic symbol followed by xyz coordiantes
::here is my file:
<pre>
BH3 molecule
B 0.00000000 0.00000000 0.00000000
H 0.00000000 1.19452732 0.00000000
H 1.03449101 -0.59726366 0.00000000
H -1.03449101 -0.59726366 0.00000000
</pre>

More on backing up and fixing your report after a crash can be found here:
[[Mod:writeup#Backing_up_your_report|fixing wiki problems]].

=Adding a link to a Gaussian job file=

==How to add a reference to a D-space file (Not for the first year lab) ==
just add {{DOI|10042/to-xyz}} where xyz is the entry generated by the publish operation into the digital repository

==How to load a file that you ran on your laptop or desktop (First years use this option!) ==
only use this option ''sparingly'' as you will fill up the available space on the server 
you should only submit pre-optimised jobs this way, that is run the optimisation to get the optimised geometry and then run a second optimisation that runs for only one step. OR only jobs that you have been explicitly told to run on your laptop. This will limit the size of the submitted file. 

First years: your file size is small enough don't worry.

choose to "Upload file" (similar to the process for images!) 
select the file on your computer 
when the file has loaded at the top of the window it will say something like: 

<pre>your_file_name.out (file size: XXX KB, MIME type: unknown/unknown) </pre>
then go to your wiki page and add something like this:
<pre>
The optimisation file is liked to [[Media:Hunt_bh3_321g_opt.log| here]]
</pre>

which looks like this:

The optimisation file is liked to [[Media:Hunt_bh3_321g_opt.log| here]]

=Tables=

Tables may at first appear complicated particularly if you have limited wiki or HTML experience however the following guide should provide you with a suitable foundation to build upon.

==A basic table==

To automatically insert a table, click or (Insert a table) on the edit toolbar. If "Insert a table" is not on the toolbar follow these directions to add it.

The following text is inserted when Insert a table is clicked:

<pre style="display: inline-block;">
{| class="wikitable" border="1"
|+ caption
! heading !! heading
|-
| cell || cell
|-
| cell || cell
|}

</pre>

By clicking ‘Preview’ you will see that the table code above will appear as follows on the wiki page:

{| class="wikitable" border="1"
|+ caption
! heading !! heading
|-
| cell || cell
|-
| cell || cell
|}

If we have a closer look at the table code you will gain a better idea of what is going on.

The entire table code is flanked by curly brackets and a pipe (vertical bar). The table begins with <code>'''{|'''</code> and is terminated using<code>'''|}'''</code>. These must be written on their own lines as follows:

'''<nowiki>{|</nowiki>'''
''table code goes here''
'''<nowiki>|}</nowiki>'''

In order to give the table a suitable title, the entry beginning with a vertical bar and plus sign "<code>'''|+'''</code>" should be used followed by your table heading textand the caption after it:

<nowiki>{|</nowiki>
'''<nowiki>|+</nowiki> ''caption'''''
''table code goes here''
<nowiki>|}</nowiki>

Additional rows can be added by typing a vertical bar and a hyphen on its own line: "<code>'''|-'''</code>".

<nowiki>{|</nowiki>
<nowiki>|+</nowiki> The table's caption
'''<nowiki>|-</nowiki>'''
''row code goes here''
'''<nowiki>|-</nowiki>'''
''next row code goes here''
<nowiki>|}</nowiki>

Following the <code>'''|-'''</code> entry, cells in the corresponding row can be separated with either a new line and a single bar for each cell in that row or by a double bar "<code>'''||'''</code>" on the same line. See the table code below as an example.
<nowiki>{|</nowiki>
<nowiki>|+</nowiki> The table's caption
<nowiki>|-</nowiki>
'''|Cell 1 || Cell 2 || Cell 3'''
<nowiki>|-</nowiki>
'''|Cell A'''
'''|Cell B'''
'''|Cell C'''
<nowiki>|}</nowiki>

It does not matter how you split the cells in row so long as you are consistent in order to avoid confusion. The table code above will be displayed as follows on your wiki page:

{|border="1" cellpadding="5" cellspacing="0" align="center"
|+ The table's caption
|-
|'''Cell 1'''||'''Cell 2'''||'''Cell 3'''
|-
|'''Cell A'''
|'''Cell B'''
|'''Cell C'''
|}

As you can see in the table above, the desired effect is the same in both cases.

==A more complicated table==

Below is the table code for a slightly more complicated table than above

<pre>

{| class="wikitable" border="1"
|+ caption
|-
! colspan="3" style="text-align: left;"|Information
|-
| colspan="3" align="center"|[[File:Benzene_3D.png|256px]]
|-
! colspan="3" style="text-align: left;"|More Info
|-
| style="text-align: center;"|Column 1
| style="text-align: center;"|Column 2
| style="text-align: center;"|Column 3
|-
| rowspan="2" | A
| colspan="2" style="text-align: center;"| B
|-
| C 
| D
|-
|  
| rowspan="2" colspan="2" style="text-align: center;" | E
|-
| F 
|-
| colspan="3" style="text-align: center;" | G
|}</pre>

The table will appear as follows:

{| class="wikitable" border="1"
|+ caption
|-
! colspan="3" style="text-align: left;"|Information
|-
| colspan="3" align="center"|[[File:Benzene_3D.png|256px]]
|-
! colspan="3" style="text-align: left;"|More Info
|-
| style="text-align: center;"|Column 1
| style="text-align: center;"|Column 2
| style="text-align: center;"|Column 3
|-
| rowspan="2" | A
| colspan="2" style="text-align: center;"| B
|-
| C 
| D
|-
|  
| rowspan="2" colspan="2" style="text-align: center;" | E
|-
| F 
|-
| colspan="3" style="text-align: center;" | G
|}

Lets have a look at some of the different commands here:

*Colspan and rowspan relate to the how many columns and rows the cell spans respectively.

*Style=”text-align: center” dictates the postioning of the text in the cell. Center can be changed for left or right depending on your preference.

*Notice that should you wish to position the image in a particular fashion then the code is slightly different to that for text:

<pre>align=”center”</pre>

*If you require a blank cell then you can use:

<pre>&nbsp;</pre>

=References=

References can be added as shown in the table below:

{| class="wikitable" border="1"
|-
! What you type
!What it looks like
|-
|<pre>
The quick brown fox jumps over the lazy dog.<ref name="LazyDog" />
<references>
<ref name="LazyDog">This is the lazy dog reference.</ref>
</references>
</pre>
|The quick brown fox jumps over the lazy dog.<ref name="LazyDog" />
<references>
<ref name="LazyDog">This is the lazy dog reference.</ref>
</references>
|}

Rep:Mod:inorganicjp2517

2019-05-23T10:58:00Z

Jp2517: /* Charge Distribution Comparison */

Rep:Mod:inorganicjp2517

2019-05-23T10:57:44Z

Jp2517: /* Charge Distribution Comparison */

Rep:Mod:inorganicjp2517

2019-05-23T10:56:24Z

Jp2517: /* Charge Distribution Comparison */

Rep:Mod:inorganicjp2517

2019-05-23T10:55:43Z

Jp2517: /* Charge Distribution Comparison */

Rep:Mod:inorganicjp2517

2019-05-23T10:52:36Z

Jp2517: /* Charge Distribution Comparison */

File:Nr4chargedist.PNG

2019-05-23T10:51:25Z

Jp2517:

File:Jp2517Pr4chargedist.PNG

2019-05-23T10:46:26Z

Jp2517:

Rep:Mod:inorganicjp2517

2019-05-23T10:45:03Z

Jp2517: /* Charge Distribution Comparison */

Rep:Mod:inorganicjp2517

2019-05-23T10:32:57Z

Jp2517: /* Optimisation */

Rep:Mod:inorganicjp2517

2019-05-23T10:31:24Z

Jp2517: /* [P(CH3)4]+ */

File:JP2517 PR4 FREQ.LOG

2019-05-23T10:30:07Z

Jp2517: