ChemWiki - User contributions [en]

Rep:Mod:isi17

2019-05-10T14:42:07Z

Isi17: /* [N(CH3)4]+ Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for BH3 Molecule

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

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

Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

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

Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP

Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

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

Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Rep:Mod:isi17

2019-05-10T14:41:39Z

Isi17: /* NH3BH3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for BH3 Molecule

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

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

Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

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

Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP

Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Rep:Mod:isi17

2019-05-10T14:41:25Z

Isi17: /* NH3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for BH3 Molecule

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

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

Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP

Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Rep:Mod:isi17

2019-05-10T14:41:09Z

Isi17: /* BH3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

Summary Table for BH3 Molecule

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP

Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Rep:Mod:isi17

2019-05-10T14:40:24Z

Isi17: /* NI3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP

Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Rep:Mod:isi17

2019-05-10T14:35:18Z

Isi17: /* Occupied Valence MOs Showing Bonding and Anti-bonding Character */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP
Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes. This MO is an anti bonding orbital.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other. This MO is an anti bonding orbital.

Rep:Mod:isi17

2019-05-10T14:26:28Z

Isi17: /* Identification of Fragment Orbitals */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP
Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other.

Rep:Mod:isi17

2019-05-10T14:25:07Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP
Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was due to the fact that Phosphorous held the highest charge of +1.667 out of any atom in either of the systems. This range was kept constant for both cations, so that direct comparisons of the charges on each atom could be made. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons (2.55) in [P(CH3)4]+ are the most electronegative atoms in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they are bonded to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T14:19:46Z

Isi17: /* NI3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===

Method: B3LYP
Basis Set: 6-31G(d,p) for Nitrogen, LanL2DZ (Pseudo Potential) for Iodine

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead. Sorry for any inconvenience.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T14:17:16Z

Isi17: /* MO Analysis of BH3 */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_LOOOL.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other.

===Identification of Fragment Orbitals===

File:01333599 BH3 MO Tricia L4 LOOOL.jpg

2019-05-10T14:16:41Z

Isi17:

Rep:Mod:isi17

2019-05-10T14:14:38Z

Isi17: /* Occupied Valence MOs Showing Bonding and Anti-bonding Character */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it. We can see sigma bonding here as 2 lobes are interacting in phase alone the bond.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node, which can be seen as the area with no electron density between the large red and green lobes, which are out of phase with each other.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T14:09:07Z

Isi17: /* Energy Calculations */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T14:06:16Z

Isi17: /* Occupied Valence MOs Showing Bonding and Anti-bonding Character */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T14:05:56Z

Isi17: /* Occupied Valence MOs Showing Bonding and Anti-bonding Character */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]
[[File:01333599_CD_MO6_AOs.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

File:01333599 CD MO6 AOs.jpg

2019-05-10T14:05:24Z

Isi17:

Rep:Mod:isi17

2019-05-10T13:53:23Z

Isi17: /* MO Analysis of BH3 */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

File:01333599 BH3 MO Tricia L4 GaussMOs FINALDIAGRAM.jpg

2019-05-10T13:52:46Z

Isi17: Isi17 uploaded a new version of File:01333599 BH3 MO Tricia L4 GaussMOs FINALDIAGRAM.jpg

Rep:Mod:isi17

2019-05-10T13:52:00Z

Isi17: /* MO Analysis of BH3 */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3 MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

File:01333599 BH3 MO Tricia L4 GaussMOs FINALDIAGRAM.jpg

2019-05-10T13:51:24Z

Isi17: Isi17 uploaded a new version of File:01333599 BH3 MO Tricia L4 GaussMOs FINALDIAGRAM.jpg

Rep:Mod:isi17

2019-05-10T13:46:40Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as the carbons in [P(CH3)4]+ are the most electronegative atom in the cation therefore hold more of the negative charge, whereas in [N(CH3)4]+ they're attached to an even more electronegative atom, nitrogen, which withdraws some electron density. [P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2 decimal places.

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T13:41:30Z

Isi17: /* NI3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

My calculation took too long to complete on the SCAN server so I have included the Optimised LOG file and Summary Table from this file instead.

Summary Table of NI3

[[File:01333599_NI3_summaryTable_Opt.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

[[File:Isi17_NI3_OPT_SCAN_pps.log]]

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

File:01333599 NI3 summaryTable Opt.jpg

2019-05-10T13:39:48Z

Isi17:

Rep:Mod:isi17

2019-05-10T13:35:56Z

Isi17: /* Inorganic Computational Lab - Iman Safia Ilyas */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

Freq Calc file:

Low freq:

Optimised N-I distance: <math> 2.187 \AA </math>

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>
</jmolApplet></jmol>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T13:33:09Z

Isi17:

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

Freq Calc file:

Low freq:

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-10T13:27:26Z

Isi17: /* Inorganic Computational Lab - Iman Safia Ilyas */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

Freq Calc file:

Low freq:

<jmol><jmolApplet>
<title>NI3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>Isi17_NI3_OPT_SCAN_pps.log</uploadedFileContents>

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

File:Isi17 NI3 OPT SCAN pps.log

2019-05-10T13:26:07Z

Isi17:

Rep:Mod:isi17

2019-05-09T14:26:37Z

Isi17: /* Occupied Valence MOs Showing Bonding and Anti-bonding Character */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

Freq Calc file:

Low freq:

jmol of freq:

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

[[File:01333599_BondingMO_MO21.jpg]]

This MO has 1 node.

===Identification of Fragment Orbitals===

File:01333599 BondingMO MO21.jpg

2019-05-09T14:24:46Z

Isi17:

Rep:Mod:isi17

2019-05-09T14:16:08Z

Isi17: /* Occupied Valence MOs Showing Bonding and Anti-bonding Character */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

Freq Calc file:

Low freq:

jmol of freq:

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

Valence MO 6

[[File:01333599_BondingMO_MO6.jpg]]

This is a bonding MO and has 2 nodes, one between the nitrogen and carbon and one between the carbon above and the hydrogen atoms attached to it.

Valence MO 15

[[File:01333599_BondingMO_MO15.jpg]]

This MO has 1 node which can be seen as the area with no electron density between the large green and red lobes.

Valence MO 21

===Identification of Fragment Orbitals===

File:01333599 BondingMO MO15.jpg

2019-05-09T14:12:37Z

Isi17:

File:01333599 BondingMO MO6.jpg

2019-05-09T14:07:40Z

Isi17:

Rep:Mod:isi17

2019-05-09T13:39:09Z

Isi17: /* NI3 Molecule */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Value Threshold Converged?
Maximum Force 0.000067 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000492 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

Freq Calc file:

Low freq:

jmol of freq:

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-09T13:17:59Z

Isi17:

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

N-H Bond Length = <math> 1.018 \AA </math>

H-N-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak, especially if we compare this to a C-C bond with bond energy of 346 kJmol-1. The B-N bond has an energy less than half the bond energy of C-C.

===NI3 Molecule===
Pseudo Potential Basis Set: 6-31G(d,p) Pseudo Potential: LanL2DZ

Summary Table of NI3

Item Table:

Freq Calc file:

Low freq:

jmol of freq

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:36:57Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used was from -1.667 to +1.667, where green represents a positive charge and the red represents a negative charge. This was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:34:30Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The sum of the partial charges is: +0.997

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The sum of the partial charges is: + 1.003

The colour range used is from -1.667 to +1.667, which was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself in the N-C bond thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

[P(CH3)4]+ has a higher overall positive charge (+1.003) than [N(CH3)4]+ (+0.997) but they both round to +1.00 if we take them at 2dp.

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:27:13Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The colour range used is from -1.667 to +1.667, which was kept constant for both cations, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective cations. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ cation as.....

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:24:27Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The colour range used is from -1.667 to +1.667, which was kept constant for both, so we can directly compare the charges on each atom. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective molecules. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as......
The charge on the hydrogen atoms is slightly more positive on the [P(CH3)4]+ molecule as.....

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:22:23Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of [N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of [P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in [N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The Charges of the Individual Atoms in [P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The colour range used is from -1.667 to +1.667. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective molecules. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in [P(CH3)4]+ than in [N(CH3)4]+ as

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:21:40Z

Isi17: /* Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295

Charge on each Carbon atom = -0.484

Charge on each Hydrogen atom = +0.269

The Charges of the Individual Atoms in P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667

Charge on each Carbon atom = -1.060

Charge on each Hydrogen atom = +0.298

The colour range used is from -1.667 to +1.667. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective molecules. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in P(CH3)4]+ than in N(CH3)4]+ as

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

Rep:Mod:isi17

2019-05-08T17:20:30Z

Isi17: /* Inorganic Computational Lab - Iman Safia Ilyas */

= Inorganic Computational Lab - Iman Safia Ilyas =

=== BH3 Molecule ===
Basis Set: 6-31G(d,p)

Method: B3LYP

[[File:01333599_SummaryTable_BH3_Freq.jpg]]

B-H Bond Length = <math> 1.192 \AA </math>

H-B-H Bond Angle = <math> 120.0</math>°

Item Value Threshold Converged?
Maximum Force 0.000009 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000034 0.001800 YES
RMS Displacement 0.000017 0.001200 YES

[[File:IMAN_BH3_FREQ.LOG]]

Low frequencies --- -2.2126 -1.0751 -0.0055 2.2359 10.2633 10.3194
Low frequencies --- 1162.9860 1213.1757 1213.1784

<jmol><jmolApplet>
<title>BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IMAN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== IR Analysis of BH3 ====

{| class="wikitable" border=1
! Mode !! Vibrations (cm-1)!! IR Active? !! Intensity (Arbitrary Units) !! Symmetry !! Bend or Stretch
|-
|1|| 1163 || Active || 93 || A2''|| Out of Plane Bend
|-
|2|| 1213 || Active || 14 || E' || Bend
|-
|3|| 1213 || Active || 14 || E' || Bend
|-
|4|| 2582 || Inactive || 0 || A1'|| Symmetric Stretch
|-
|5|| 2715 || Active || 126 || E' || Asymmetric Stretch
|-
|6|| 2715 || Active || 126 || E'|| Asymmetric Stretch
|}

[[File:01333599_IR_Spectrum_Freqlog.jpg]]

There are less than 6 peaks in the spectrum although there are 6 modes of vibration. This is because not all modes are IR active. To be IR active there must be a change in dipole moment. Mode 4 is a symmetric stretch therefore is not IR active and is therefore not visible on the spectrum. The vibrations of modes 2 and 3 have frequencies very close to each other and therefore overlap showing one prominent peak. The same thing occurs for modes 5 and 6. The third peak is for Mode 1.

==== MO Analysis of BH3 ====

[[File:01333599_BH3_MO_Tricia_L4_GaussMOs_FINALDIAGRAM.jpg]]

(MO Diagram for BH3, Lecture 4 Tutorial Problem Model Answers, P. Hunt, Accessed 08/05/19 [http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf])

There are differences between the real MOs and the MOs predicted by LCAO, but they are not significant. Both have areas of high electron density and no electron density. Areas with no electron density represent nodes. By seeing the comparison between the real MOs and those predicted by LCAO, it can be said that MO theory is very accurate and useful. the differences are mainly the shape of the orbitals themselves. These are more distorted in the real MOs computed by gaussian.

=== NH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3

[[File:01333599_NH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.018 \AA </math>

H-B-H Bond Angle = <math> 105.7 </math>°

Item Value Threshold Converged?
Maximum Force 0.000005 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000006 0.001200 YES

[[File:ISI17_NH3_FREQ_631G.LOG]]

Low frequencies --- -11.6527 -11.6490 -0.0048 0.0332 0.1312 25.5724
Low frequencies --- 1089.6616 1694.1736 1694.1736

<jmol><jmolApplet>
<title>NH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3_FREQ_631G.LOG</uploadedFileContents>
</jmolApplet></jmol>

=== NH3BH3 Molecule ===

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table for NH3BH3

[[File:01333599_NH3BH3_SummaryTable_Freq.jpg]]

B-H Bond Length = <math> 1.019 \AA </math>

N-H Bond Length = <math> 1.210 \AA </math>

B-N Bond Length = <math> 1.668 \AA </math>

H-B-H Bond Angle = <math> 107.9 </math>°

H-N-H Bond Angle = <math> 113.9 </math>°

H-B-N Bond Angle = <math> 111.0 </math>°

H-N-B Bond Angle = <math> 104.6 </math>°

Item Value Threshold Converged?
Maximum Force 0.000139 0.000450 YES
RMS Force 0.000063 0.000300 YES
Maximum Displacement 0.000771 0.001800 YES
RMS Displacement 0.000338 0.001200 YES

[[File:ISI17_NH3BH3_FREQ.LOG]]

Low frequencies --- -0.0010 -0.0006 0.0005 19.1023 23.7761 42.9934
Low frequencies --- 266.5969 632.3818 639.5198

<jmol><jmolApplet>
<title>NH3BH3 Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Energy Calculations===

<math>E(BH_3) = -26.61532363 au </math>

<math>E(NH_3) = -56.55776856 au </math>

<math>E(BH_3NH_3) = -83.22469009 au </math>

Association Energy: <math> \Delta E = E(NH_3BH_3) - (E(NH_3) + E(BH_3)) = -0.0515979 au </math>

Converting from au to kJmol-1 :

<math> (-0.0515979)(2625.5) = -135.4702865 </math>

<math> \Delta E = -135 kJmol^{-1} </math>

We can see that the N-B bond is relatively weak. If we compare this to a C-C bond with bond energy of 346 kJmol-1. This is less than half the strength of C-C.

===NI3 Molecule===

== Project: Ionic Liquids ==

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

Basis Set: 6-31G(d,p)
Method: B3LYP

Summary Table of [N(CH3)4]+

[[File:01333599_N(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000072 0.000450 YES
RMS Force 0.000029 0.000300 YES
Maximum Displacement 0.000178 0.001800 YES
RMS Displacement 0.000079 0.001200 YES

[[File:ISI17_-N(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0011 -0.0007 -0.0007 35.5217 35.5217 35.5217
Low frequencies --- 217.0556 316.2155 316.2155

<jmol><jmolApplet>
<title>[N(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-N(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

Method: B3LYP

Summary Table of [P(CH3)4]+

[[File:01333599_P(CH3)4_SummaryTable_Freq.jpg]]

Item Value Threshold Converged?
Maximum Force 0.000095 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.001541 0.001800 YES
RMS Displacement 0.000494 0.001200 YES

[[File:ISI17_-P(CH3)4-_FREQ_01333599.LOG]]

Low frequencies --- -0.0003 0.0018 0.0026 13.7497 22.4514 35.0103
Low frequencies --- 162.9535 193.8816 195.5982

<jmol><jmolApplet>
<title>[P(CH3)4]+ Molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISI17_-P(CH3)4-_FREQ_01333599.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distributions of [N(CH3)4]+ and [P(CH3)4]+ ===

Image 1: Shows Charge Distribution of N(CH3)4]+

[[File:01333599_N(CH3)4_Charge_Distribution.jpg]]

Image 2: Shows Charge Distribution of P(CH3)4]+

[[File:01333599_P(CH3)4_Charge_Distribution.jpg]]

The Charges of the Individual Atoms in N(CH3)4]+ are:

Charge on the Nitrogen atom = -0.295
Charge on each Carbon atom = -0.484
Charge on each Hydrogen atom = +0.269

The Charges of the Individual Atoms in P(CH3)4]+ are:

Charge on the Phosphorous atom = +1.667
Charge on each Carbon atom = -1.060
Charge on each Hydrogen atom = +0.298

The colour range used is from -1.667 to +1.667. It can be seen that the Phosphorous atom holds a much more positive charge than the nitrogen in their respective molecules. This can be explained as Nitrogen (3.04) is a much more electronegative element than Phosphorous (2.19) on the Pauling scale. this means that Nitrogen is more likely to pull the electron density towards itself thus having a more negative charge on the atom. The charge is also more negative on the carbon atoms in P(CH3)4]+ than in N(CH3)4]+ as

''[['''ASK DEMONSTRATOR''']]''

===Validity of Traditional Description of [N(CH3)4]+===

If we look at the traditional description, the formal charge is said to be localised solely on the nitrogen atom, however, it can be seen that it actually holds part of a negative charge. The positive charge is spread around the outside of the molecule as it is delocalised around the hydrogen atoms. The Hydrogen atoms are where the actual positive charge is located for this molecule.

===Occupied Valence MOs Showing Bonding and Anti-bonding Character===

===Identification of Fragment Orbitals===

File:01333599 P(CH3)4 Charge Distribution.jpg

2019-05-08T17:03:57Z

Isi17:

File:01333599 N(CH3)4 Charge Distribution.jpg

2019-05-08T17:02:02Z

Isi17:

Rep:Mod:isi17

2019-05-08T15:42:30Z

Isi17: /* Inorganic Computational Lab - Iman Safia Ilyas */

Rep:Mod:isi17

2019-05-08T15:37:13Z

Isi17: /* Inorganic Computational Lab - Iman Safia Ilyas */

File:ISI17 -P(CH3)4- FREQ 01333599.LOG

2019-05-08T15:35:19Z

Isi17:

File:01333599 P(CH3)4 SummaryTable Freq.jpg

2019-05-08T15:34:03Z

Isi17:

Rep:Mod:isi17

2019-05-08T15:19:04Z

Isi17: /* Inorganic Computational Lab - Iman Safia Ilyas */

Rep:Mod:isi17

2019-05-08T15:17:46Z

Isi17: /* [N(CH3)4]+ Molecule */

File:ISI17 -N(CH3)4- FREQ 01333599.LOG

2019-05-08T15:17:19Z

Isi17: