ChemWiki - User contributions [en]

Rep:Mod:inorganic DY2917

2019-05-24T14:05:01Z

Dy2917: /* Charge Distribution */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NBO Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NBO Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+(R=alkyl)===
Q: What does the "formal" positive charge on the N represent in the traditional picture?

The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

Q:On what atoms is the positive charge actually located for this cation?

Due to the electronegativity of atoms as shown above, hydrogen, which has the lowest electronegativity, would be where the +1 charge is spread out and located.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Prof. Patricia Hunt,'Figure 5' on Lecture_4_Tut_MO_diagram_BH3.

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-24T14:04:45Z

Dy2917: /* Charge Distribution */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NBO Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+(R=alkyl)===
Q: What does the "formal" positive charge on the N represent in the traditional picture?

The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

Q:On what atoms is the positive charge actually located for this cation?

Due to the electronegativity of atoms as shown above, hydrogen, which has the lowest electronegativity, would be where the +1 charge is spread out and located.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Prof. Patricia Hunt,'Figure 5' on Lecture_4_Tut_MO_diagram_BH3.

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-24T14:03:14Z

Dy2917: /* Reference */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+(R=alkyl)===
Q: What does the "formal" positive charge on the N represent in the traditional picture?

The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

Q:On what atoms is the positive charge actually located for this cation?

Due to the electronegativity of atoms as shown above, hydrogen, which has the lowest electronegativity, would be where the +1 charge is spread out and located.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Prof. Patricia Hunt,'Figure 5' on Lecture_4_Tut_MO_diagram_BH3.

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T16:20:19Z

Dy2917: /* Charge Distribution of [NR4]+(R=alkyl) */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+(R=alkyl)===
Q: What does the "formal" positive charge on the N represent in the traditional picture?

The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

Q:On what atoms is the positive charge actually located for this cation?

Due to the electronegativity of atoms as shown above, hydrogen, which has the lowest electronegativity, would be where the +1 charge is spread out and located.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T16:20:08Z

Dy2917: /* Charge Distribution of [NR4]+(R=alkyl) */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+(R=alkyl)===
Q: What does the "formal" positive charge on the N represent in the traditional picture?
The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

Q:On what atoms is the positive charge actually located for this cation?
Due to the electronegativity of atoms as shown above, hydrogen, which has the lowest electronegativity, would be where the +1 charge is spread out and located.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T16:17:53Z

Dy2917: /* Charge Distribution of [NR4]+ */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+(R=alkyl)===
Q: What does the "formal" positive charge on the N represent in the traditional picture?
The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

Q:

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T16:16:58Z

Dy2917: /* Charge Distribution of [NR4]+ */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===
Q: What does the "formal" positive charge on the N represent in the traditional picture?
The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions of Nitrogen with the attached groups, the +1 charge would be distributed among the atoms according to their electronegativity.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T16:15:16Z

Dy2917: /* Charge Distribution of [NR4]+ */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===
Q: What does the "formal" positive charge on the N represent in the traditional picture?
The electronic configuration of the nitrogen is 1s22s22p3. 5 valence electrons in total. 3 of these electrons are used for the covalant-bond between R groups. This leaves another 2 electron (lone pair) which is forming a dative bond with the 4th R group. The 2 electrons from the Nitrogen is then shared between N atom and R, which leads to an electron deficient on the Nitrogen atom and thereby positively charged. However, due to the interactions within different atoms on the molecule, the +1 charge would then be distributed among all the atoms according to their electronegativity.

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T16:07:26Z

Dy2917: /* Charge Distribution of [NR4]+ */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===
Q

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:59:31Z

Dy2917: /* Molecular orbital 3 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
This MO only shows bonding character, no anti-bonding character is presented here.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:58:55Z

Dy2917: /* Molecular orbital 3 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO3 FO.PNG]]

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

File:DY2917 MO3 FO.PNG

2019-05-23T15:58:44Z

Dy2917:

Rep:Mod:inorganic DY2917

2019-05-23T15:56:12Z

Dy2917: /* Molecular orbital 3 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:52:19Z

Dy2917: /* Molecular orbital 3 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO3_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO3_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO3_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

File:DY2917 MO3 3.PNG

2019-05-23T15:51:43Z

Dy2917:

File:DY2917 MO3 2.PNG

2019-05-23T15:51:29Z

Dy2917:

File:DY2917 MO3 1.PNG

2019-05-23T15:51:14Z

Dy2917:

Rep:Mod:inorganic DY2917

2019-05-23T15:49:05Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below. No bonding character can be seen in this MO.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:48:33Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.

As can be easily seen from the z-axis projectory, there is antibonding character between the frontier p-orbital at the top and the one below.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:47:38Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.
As can be easily seen from the z-axis projectory, there is antibonding character between the upper frontier p-orbital and the one below.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:46:00Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.

All interactions in this MO are bonding interactions.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:45:33Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO2.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

File:DY2917 MO1 FO2.PNG

2019-05-23T15:45:13Z

Dy2917:

Rep:Mod:inorganic DY2917

2019-05-23T15:14:52Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:14:02Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===

This belong to the No.16 MO from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T15:13:24Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===

{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}
[[File:DY2917 MO2 FO.PNG]]

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

File:DY2917 MO2 FO.PNG

2019-05-23T15:12:49Z

Dy2917:

Rep:Mod:inorganic DY2917

2019-05-23T14:57:09Z

Dy2917: /* Molecular orbital 3 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO2_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO2_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO2_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

File:DY2917 MO2 3.PNG

2019-05-23T14:55:40Z

Dy2917:

File:DY2917 MO2 2.PNG

2019-05-23T14:55:25Z

Dy2917:

File:DY2917 MO2 1.PNG

2019-05-23T14:55:12Z

Dy2917:

Rep:Mod:inorganic DY2917

2019-05-23T14:54:51Z

Dy2917: /* Molecular orbital 3 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

===Molecular orbital 3===
{| class="wikitable" border="1"
|+ Visualised MO 3
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:54:42Z

Dy2917: /* Molecular orbital 2 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===
{| class="wikitable" border="1"
|+ Visualised MO 2
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:48:11Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

This belong to the No.21 MO(HOMO) from GaussView.
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:46:30Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

[[File:DY2917 MO1 FO.PNG]]

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

File:DY2917 MO1 FO.PNG

2019-05-23T14:46:12Z

Dy2917:

Rep:Mod:inorganic DY2917

2019-05-23T14:45:15Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| Projected from the y-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb| Projected from the x-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb| Projected from the z-direction]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:10:46Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|none]] || [[File:DY2917_MO1_2.PNG|250px|none]] || [[File:DY2917_MO1_3.PNG|250px|none]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:08:45Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px|thumb| x-direction]] || [[File:DY2917_MO1_2.PNG|250px|thumb|y-direction]] || [[File:DY2917_MO1_3.PNG|250px|thumb|z-direction]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:07:47Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px]] || [[File:DY2917_MO1_2.PNG|250px]] || [[File:DY2917_MO1_3.PNG|150px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:06:40Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|250px]] || [[File:DY2917_MO1_2.PNG|250px]] || [[File:DY2917_MO1_3.PNG|250px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:06:18Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|300px]] || [[File:DY2917_MO1_2.PNG|300px]] || [[File:DY2917_MO1_3.PNG|300px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:06:02Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|300px]] || [[File:DY2917_MO1_2.PNG|300px]] || [[File:DY2917_MO1_3.PNG|200px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:05:44Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|300px]] || [[File:DY2917_MO1_2.PNG|300px]] || [[File:DY2917_MO1_3.PNG|300px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:05:24Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ caption
! Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG|300px]] || [[File:DY2917_MO1_2.PNG|300px]] || [[File:DY2917_MO1_3.PNG|300px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:05:11Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ caption
! Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG||300px]] || [[File:DY2917_MO1_2.PNG||300px]] || [[File:DY2917_MO1_3.PNG||300px]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:04:36Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ caption
! Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG]] || [[File:DY2917_MO1_2.PNG]] || [[File:DY2917_MO1_3.PNG]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:04:09Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ caption
! Visualised MO 1
|-
| [[File:DY2917_MO1_1.PNG]] || [[File:DY2917_MO1_2.PNG]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:03:51Z

Dy2917: /* Molecular orbital 1 */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===
{| class="wikitable" border="1"
|+ caption
! Visualised MO 1
|-
| [[File:DY2917_MO_1.PNG]] || [[File:DY2917_MO_2.PNG]]
|}

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.

Rep:Mod:inorganic DY2917

2019-05-23T14:01:27Z

Dy2917: /* MO section */

=Calculating the association energy of Ammonia-Borane=

==BH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0009 0.0280 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392
</pre>
====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>
====Optimisation link====

Frequency file: [[Media:DP_BH3_FREQ_3.LOG| BH3_frequency.log]]

===J-mol (BH3) ===

<jmol><jmolApplet>
<title>BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DP_BH3_FREQ_3.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational spectrum===
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|very slight
|bend
|-
|1213
|14
|E
|very slight
|bend
|-
|2583
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:DY2917 BH3 Spectrum.PNG]]

There are 6 vibrational modes, however, only 3 are shown on the spectrum. Mode 2,3 and 5,6 are degenerate in energy, therefore, 4 peaks should be observed, (2,3) shown as one peak, (5,6) shown as another. Since mode 4 is symmetric stretch, it would have a net dipolar moment of 0, hence, will not be observed on the spectrum.

===Molecular orbital===

[[File:DY2917 BH3 MO attached.PNG|none|thumb|MO diagram of BH3[1].]]

<li>Are there any significant differences between the real and LCAO MOs? </li>

The molecular orbital predicted from LCAO is pretty similar to the real MOs calculated. However, for 3a', the real MO shows a cylinder shaped orbital at the centre while LCAO predicted it to be a sphere.

<li>What does this say about the accuracy and usefulness of qualitative MO theory? </li>

It suggest the highly accuracy of MO theory, despite from some little differences like stated above, it is still a really useful method to predict the Molecular orbitals.

==NH3 section==

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0129 -0.0018 -0.0016 7.0724 8.1020 8.1023
Low frequencies --- 1089.3849 1693.9369 1693.9369
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000013 0.001800 YES
RMS Displacement 0.000007 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 NH3 FREQ 2.LOG| NH3_frequency.log]]

===J-mol (NH3)===

<jmol><jmolApplet>
<title>NH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==NH3BH3 Section==
===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_NH3BH3_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0277 -0.0068 -0.0052 10.0740 10.1217 37.8835
Low frequencies --- 265.3010 634.4256 639.2067
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000349 0.000450 YES
RMS Force 0.000111 0.000300 YES
Maximum Displacement 0.001345 0.001800 YES
RMS Displacement 0.000449 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NH3BH3_FREQ_2.LOG| NH3BH3_frequency.log]]

===J-mol (NH3BH3)===

<jmol><jmolApplet>
<title>NH3BH3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NH3BH3_FREQ_2.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Energy==
<li>E(NH3)= -26.61532 a.u.
<li>E(BH3)= -56.55777 a.u.
<li>E(NH3BH3)= -83.22469 a.u.
<pre>
ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=[-83.22469-(-56.55777-26.61532)]a.u.
=-0.0516 a.u.
=-135 kJ/mol
</pre>

The dissociation energy of the B-N dative bond is -135 KJ/mol

Bond energies[2]
<pre>
C-C single bond 348 KJ/mol
B-B single bond 293 KJ/mol
C-N single bond 305 KJ/mol
</pre>
BY comparison, it indicates that the B-N dative bond is a relatively weak bond.

=PPs and basis-sets of NI3=

===Summary Table===

Method used: B3LYP

Basis set used: GEN [6-31G(d,p) for N, LanL2DZ for I]

[[File:DY2917_NI3_Summary.PNG]]

The optimised distance for NI3 is 2.184 Å.

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0576 -0.0292 -0.0031 1.9682 2.0035 2.2189
Low frequencies --- 101.3080 101.3087 148.3159
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000028 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000242 0.001800 YES
RMS Displacement 0.000122 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917_NI3_FREQ.LOG| NI3_frequency.log]]

===J-mol (NI3)===

<jmol><jmolApplet>
<title>NI3molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=Mini Project: Ionic Liquid=

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_N(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- -0.0011 0.0008 0.0009 22.8070 22.8070 22.8070
Low frequencies --- 189.0756 292.9198 292.9198
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000036 0.000450 YES
RMS Force 0.000015 0.000300 YES
Maximum Displacement 0.000264 0.001800 YES
RMS Displacement 0.000146 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 N(CH3)4 FREQ TD.LOG| [N(CH3)4]+_frequency.log]]

===J-mol ([N(CH3)4]+)===

<jmol><jmolApplet>
<title>[N(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 N(CH3)4 FREQ TD.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 N(CH3)4 charge.PNG|none|thumb|Charge distribution of [N(CH3)4;colour range ±o.5]+]]

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

===Summary Table===

Method used: B3LYP

Basis set used: 6-31G(d,p)

[[File:DY2917_P(CH3)4_Summary.PNG]]

===Frequency and Optimisation Table===

====Frequency table====
<pre>
Low frequencies --- 0.0005 0.0012 0.0012 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740
</pre>

====Optimisation table====
<pre>
Item Value Threshold Converged?
Maximum Force 0.000027 0.000450 YES
RMS Force 0.000022 0.000300 YES
Maximum Displacement 0.000436 0.001800 YES
RMS Displacement 0.000388 0.001200 YES
</pre>

====Optimisation link====

Frequency file: [[Media:DY2917 P(CH3)4 FREQ.LOG| [P(CH3)4]+_frequency.log]]

===J-mol ([P(CH3)4]+)===

<jmol><jmolApplet>
<title>[P(CH3)4]+molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>DY2917 P(CH3)4 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Charge Distribution===
[[File:DY2917 P(CH3)4 charge.PNG|none|thumb|Charge distribution of [P(CH3)4]+; colour range ±0.5]]

==Charge Distribution Section==
===Comparison of the charge distribution of [P(CH3)4]+ with [N(CH3)4]+===
{| class="wikitable"
|+
|-
|[[File:DY2917 P(CH3)4 charge.PNG|200px|thumb|Charge distribution of [P(CH3)4]+]]
||[[File:DY2917 N(CH3)4 charge.PNG|200px|thumb|Charge distribution of [N(CH3)4]+]]
|}

<li> The Pauling electronegativity of P, C, N and H are 2.19, 2.55, 3.04 and 2.20 respectively.[3]
<li> Electronegativity is a measure of the tendency of an atom to pull the shared pair of electron towards itself.
<li> As indicated above, the Nitrogen is the most electronegative, followed by Carbon, hydrogen and then phosphorus.</li>
Therefore:
<li> [N(CH3)4]+ ion: Nitrogen should have the most negative charge, followed by Carbon and then Hydrogen which is positively charged. However, the +1 charge is possessed on the Nitrogen, which hence, would raise the relative charge distribution of the Nitrogen and make it less negative.</li>
<li> [P(CH3)4]+ ion: P and H have similar electronegativity, both less than Carbon. The +1 charge is possessed on the P atom, this suggest that P would have a large positive charge distribution with carbon having a relative small negative charge and hydrogen being slightly positive.</li>
<li> As can be seen from the two charge distributions:</li>
in the [P(CH3)4]+ ion, P has a large positive charge of +1.667, C has a negative value of -1.060 and H being +0.298;
in the [N(CH3)4]+ ion, N has a small negative charge of -0.295, C has a large negative value of -0.483 and H being +0.269.
<li> In summary, the displayed value met with the interpretation above.

===Charge Distribution of [NR4]+===

==MO section==
===Molecular orbital 1===

===Molecular orbital 2===

===Molecular orbital 3===

=Reference=

1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

3.A.M. James and M.P. Lord in Macmillan's Chemical and Physical Data, Macmillan, London, UK, 1992.