ChemWiki - User contributions [en]

Ly617

2019-05-20T16:56:44Z

Ly617:

== Introduction ==

This lab constructs molecule or complex models using Gaussview, optimises the models and runs frequencies analysis on them via calculation. By doing so, the bonding and anti-bonding of the molecules or complexes, their structures, vibration modes and MOs can be visualised and used for further investigation. In this lab, the molecules BH3, NH3, NH3BH3, NI3, and the cations [N(CH3)4]+ and [N(CH3)4]+ are analysed.

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1164 || 93 || Yes || bending || out of plane || A2
|-
| 2 || 1214 || 14 || Yes || bending || in plane || E'
|-
| 3 || 1214 || 14 || Yes || bending || in plane || E'
|-
| 4 || 2580 || 0 || No || stretching || symmetric || A1'
|-
| 5 || 2713 || 126 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713 || 126 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the individual AOs, and it can be used as reference of the real MOs. LCAO MOs contains lobes with different phases, which represents the s and p orbitals of atoms, and simple lines representing the bond between adjacent atoms. In LCAO MOs, the AOs stay separated from each other. In real MOs, the exact sizes of orbitals are described. The orbitals with the same phases can merge, showing the overlap of the AOs.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MOs depends on the level of complication of the molecules. For the MOs of the molecules with less atoms, LCAO MOs can describe the MOs more clearly and overlap of AOs can be predicted easily. For larger molecules, the LCAO MOs are disabled in many aspects, for example visualising the AOs is becoming complicated and fails to show the overlap of the AOs. But still LCAO is a reliable prediction of the real MO hence is quite useful.
----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

== Conclusion ==

The diversity of analysed complexes in this lab indicated that this calculation method could be widely used in many systems to visualise the optimised structure, properties and frequencies of many molecules for further information about the MOs and bond energies.

Ly617

2019-05-20T16:43:09Z

Ly617: /* Frequency Analysis of BH3 */

Ly617

2019-05-20T16:41:19Z

Ly617: /* Introduction */

== Introduction ==

This lab constructs molecule or complex models using Gaussview, optimises the models and runs frequencies analysis on them via calculation. By doing so, the bonding and anti-bonding of the molecules or complexes, their structures, vibration modes and MOs can be visualised and used for further investigation. In this lab, the molecules BH3, NH3, NH3BH3, NI3, and the cations [N(CH3)4]+ and [N(CH3)4]+ are analysed.

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the individual AOs, and it can be used as reference of the real MOs. LCAO MOs contains lobes with different phases, which represents the s and p orbitals of atoms, and simple lines representing the bond between adjacent atoms. In LCAO MOs, the AOs stay separated from each other. In real MOs, the exact sizes of orbitals are described. The orbitals with the same phases can merge, showing the overlap of the AOs.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MOs depends on the level of complication of the molecules. For the MOs of the molecules with less atoms, LCAO MOs can describe the MOs more clearly and overlap of AOs can be predicted easily. For larger molecules, the LCAO MOs are disabled in many aspects, for example visualising the AOs is becoming complicated and fails to show the overlap of the AOs. But still LCAO is a reliable prediction of the real MO hence is quite useful.
----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T16:40:43Z

Ly617: /* Introduction */

== Introduction ==

This lab constructs molecule or complex models using Gaussview, optimises the models and runs frequencies analysis on them via calculation. By doing so, the bonding of the molecules or complexes, their structures, vibration modes and MOs can be visualised and used for further investigation. In this lab, the molecules BH3, NH3, NH3BH3, NI3, and the cations [N(CH3)4]+ and [N(CH3)4]+ are analysed.

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the individual AOs, and it can be used as reference of the real MOs. LCAO MOs contains lobes with different phases, which represents the s and p orbitals of atoms, and simple lines representing the bond between adjacent atoms. In LCAO MOs, the AOs stay separated from each other. In real MOs, the exact sizes of orbitals are described. The orbitals with the same phases can merge, showing the overlap of the AOs.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MOs depends on the level of complication of the molecules. For the MOs of the molecules with less atoms, LCAO MOs can describe the MOs more clearly and overlap of AOs can be predicted easily. For larger molecules, the LCAO MOs are disabled in many aspects, for example visualising the AOs is becoming complicated and fails to show the overlap of the AOs. But still LCAO is a reliable prediction of the real MO hence is quite useful.
----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T16:27:28Z

Ly617:

== Introduction ==

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the individual AOs, and it can be used as reference of the real MOs. LCAO MOs contains lobes with different phases, which represents the s and p orbitals of atoms, and simple lines representing the bond between adjacent atoms. In LCAO MOs, the AOs stay separated from each other. In real MOs, the exact sizes of orbitals are described. The orbitals with the same phases can merge, showing the overlap of the AOs.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MOs depends on the level of complication of the molecules. For the MOs of the molecules with less atoms, LCAO MOs can describe the MOs more clearly and overlap of AOs can be predicted easily. For larger molecules, the LCAO MOs are disabled in many aspects, for example visualising the AOs is becoming complicated and fails to show the overlap of the AOs. But still LCAO is a reliable prediction of the real MO hence is quite useful.
----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T15:24:52Z

Ly617: /* The MO Diagram of BH3 */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the individual AOs, and it can be used as reference of the real MOs. LCAO MOs contains lobes with different phases, which represents the s and p orbitals of atoms, and simple lines representing the bond between adjacent atoms. In LCAO MOs, the AOs stay separated from each other. In real MOs, the exact sizes of orbitals are described. The orbitals with the same phases can merge, showing the overlap of the AOs.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MOs depends on the level of complication of the molecules. For the MOs of the molecules with less atoms, LCAO MOs can describe the MOs more clearly and overlap of AOs can be predicted easily. For larger molecules, the LCAO MOs are disabled in many aspects, for example visualising the AOs is becoming complicated and fails to show the overlap of the AOs. But still LCAO is a reliable prediction of the real MO hence is quite useful.
----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:47:17Z

Ly617: /* [P(CH3)4]+ */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:46:57Z

Ly617: /* [N(CH3)4]+ */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:46:44Z

Ly617: /* NI3 */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 Molecule ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:46:33Z

Ly617: /* NH3BH3 */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 Molecule ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:46:20Z

Ly617: /* NH3 */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 Molecule ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:46:07Z

Ly617: /* BH3 */

==Revision==

=== BH3 Molecule ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:45:26Z

Ly617: /* Charge Distribution */

==Revision==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom. The behaviour is due to the lower electronegativity of P and H (P = H = 2.1) comparing to that of atom C (2.5).

Range = -0.500 to 0.500

Ly617

2019-05-20T14:42:39Z

Ly617: /* Charge Distribution */

==Revision==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-20T14:42:16Z

Ly617: /* Charge Distribution */

==Revision==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge than N. That is because C and N are more electronegative than H. In traditional way, the positive charge is drawn next to and located on the N atom since it is the centre of the molecule. However the charge distribution analysis indicates that the positive charge is distributed on H.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-20T14:32:51Z

Ly617: /* Frequency Analysis of BH3 */

==Revision==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry Type !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane || A2
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane || E'
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric || A1'
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric || E'
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-20T14:08:27Z

Ly617: /* Frequencies Analysis of NH3 */

==Revision==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Media:LY_NH3_FREQ2.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

File:LY NH3 FREQ2.LOG

2019-05-20T14:07:58Z

Ly617:

File:LY NH3 FREQ.LOG

2019-05-20T14:06:41Z

Ly617: Ly617 uploaded a new version of File:LY NH3 FREQ.LOG

Ly617

2019-05-20T14:04:02Z

Ly617: /* Day 1 */

==Revision==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-17T15:59:49Z

Ly617: /* The MO Diagram of BH3 */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

The MOs diagram of BH3 from Hunt Research Group's website: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.<ref name="The MOs diagram of BH3" />
<references>
<ref name="The MOs diagram of BH3">This is the MOs of BH3 reference.</ref>
</references>

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-17T15:54:57Z

Ly617: /* Mini Project: Ionic Liquids */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-17T15:54:26Z

Ly617: /* [N(CH3)4]+ */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

File:LY MO10.PNG

2019-05-17T15:53:46Z

Ly617: Ly617 uploaded a new version of File:LY MO10.PNG

File:LY MO10.PNG

2019-05-17T15:51:08Z

Ly617: Ly617 uploaded a new version of File:LY MO10.PNG

Ly617

2019-05-17T15:47:48Z

Ly617: /* MOs */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REALMO.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

File:LY MO10 REALMO.PNG

2019-05-17T15:47:06Z

Ly617:

Ly617

2019-05-17T15:41:02Z

Ly617: /* Charge Distribution */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REAL.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.The positive charge is distributed on P and H because they’re both less electronegative (P = H = 2.1) than atom C (2.5), on which the negative charge is on.

Range = -0.500 to 0.500

Ly617

2019-05-17T15:38:12Z

Ly617: /* Charge Distribution */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge. That is because C (2.5) and N (3.0) are more electronegative than H (2.1).

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REAL.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

Ly617

2019-05-17T15:30:45Z

Ly617: /* MO=10 */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

==== MOs ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REAL.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

Ly617

2019-05-17T15:29:55Z

Ly617: /* MO=10 */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

==== MOs ====

==== MO=10 ====

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied? !! Bonding Character
|-
| MO = 10 || [[File:LY_MO10_REAL.PNG]] || [[File:LY_MO10.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes || bonding
|-
| MO = 16 || [[File:LY_MO16_REAL.PNG]] || [[File:LY_MO16.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes || bonding
|-
| MO = 21 || [[File:LY_MO21_REAL.PNG]] || [[File:LY_MO21.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes || bonding
|}

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

File:LY MO21 REAL.PNG

2019-05-17T15:26:03Z

Ly617:

File:LY MO21.PNG

2019-05-17T15:25:53Z

Ly617:

File:LY MO16 REAL.PNG

2019-05-17T15:25:44Z

Ly617:

File:LY MO16.PNG

2019-05-17T15:25:35Z

Ly617:

Ly617

2019-05-17T15:18:01Z

Ly617: /* MO=10 */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

==== MOs ====

==== MO=10 ====

[[File:LY_MO10_REAL.PNG|thumb|left|The MO diagram of MO=10]]

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

File:LY MO10.PNG

2019-05-17T15:17:50Z

Ly617: Ly617 uploaded a new version of File:LY MO10.PNG

Ly617

2019-05-17T14:13:27Z

Ly617: /* MOs */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

==== MOs ====

==== MO=10 ====

[[File:LY_MO10_REAL.PNG|thumb|The MO diagram of MO=10]]

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

File:LY MO10.PNG

2019-05-17T14:02:18Z

Ly617:

File:MO10 REAL.PNG

2019-05-17T14:00:28Z

Ly617:

Ly617

2019-05-17T13:54:36Z

Ly617:

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

==== MOs ====

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

Ly617

2019-05-16T16:27:26Z

Ly617: /* Charge Distribution */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

Ly617

2019-05-16T16:27:02Z

Ly617: /* Charge Distribution */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

Ly617

2019-05-16T16:26:27Z

Ly617: /* Mini Project: Ionic Liquids */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_N(CH3)4_CHARGE.PNG|thumb|The charge distribution of [N(CH3)4]+]]

Charge of N = -0.295

Charge of C = -0.483

Charge of H = +0.269

The positive charge is completely distributed on H atoms. The negative charge is on N and C atoms, while C atoms have larger distribution of the charge.

Range = -0.500 to 0.500

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

File:LY N(CH3)4 CHARGE.PNG

2019-05-16T16:23:41Z

Ly617:

Ly617

2019-05-16T16:09:48Z

Ly617: /* Charge Distribution */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom.

Range = -0.500 to 0.500

Ly617

2019-05-16T16:06:07Z

Ly617: /* Charge Distribution */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

Charge of P = +1.667

Charge of C = -1.050

Charge of H = +0.298

The positive charge is mainly distributed on P atom and slightly on H atoms. The negative charge is on C atom

File:LY P(CH3)4 CHARGE.PNG

2019-05-16T16:04:44Z

Ly617: Ly617 uploaded a new version of File:LY P(CH3)4 CHARGE.PNG

Ly617

2019-05-16T15:41:52Z

Ly617: /* [P(CH3)4]+ */

==Day 1==

=== BH3 ===

==== B3LYP/3-21G ====

[[File:LY_BH3_OPT_321_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 3-21G basis set]]

Item Value Threshold Converged?
Maximum Force 0.000217 0.000450 YES
RMS Force 0.000105 0.000300 YES
Maximum Displacement 0.000919 0.001800 YES
RMS Displacement 0.000441 0.001200 YES

The total energy = -26.46226371 a.u.

[[File:LY_BH3_OPT_321_ENERGY.PNG|The energy change during the optimisation of BH3]]

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

[[File:LY_BH3_OPT_631_SUM.PNG|thumb|left|The summary table of optimised BH3 molecule using 6-31G(d,p) basis set]]

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000867 0.001800 YES
RMS Displacement 0.000415 0.001200 YES

The total energy = -26.61532350 a.u.

'''Jmol image of BH3:'''
<jmol><jmolApplet>
<title>BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of BH3 ====

[[File:LY_BH3_OPT_FREQ_SUM.PNG ‎|thumb|left|The summary table of frequencies of BH3 molecule using 6-31G(d,p) basis set]]

Frequency analysis log file [[Media:LY_BH3_FREQ.LOG]]

Low frequencies --- -0.2456 -0.1129 -0.0054 44.0270 45.1846 45.1853
Low frequencies --- 1163.6049 1213.5924 1213.5951

[[File:LY_BH3_FREQ_SPECTRUM.PNG|thumb|left|800px|The IR spectrum of vibrations of BH3 molecule]] [[File:LY_BH3_Frequencies.PNG|frame|centre|1000px|The frequencies of vibration modes of BH3 molecule]]

{| class="wikitable" border=1
! Mode !! Frequency !! Intensity !! IR active? !! Type of vibration !! Symmetry
|-
| 1 || 1163.6 || 92.48 || Yes || bending || out of plane
|-
| 2 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 3 || 1213.6 || 14.08 || Yes || bending || in plane
|-
| 4 || 2580.2 || 0.00 || No || stretching || symmetric
|-
| 5 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|-
| 6 || 2713.1 || 126.40 || Yes || stretching || asymmetric
|}

There are totally 6 vibration modes, but from the IR spectrum only 3 peaks can be observed, which are 1163.6 cm-1, 1213.6 cm-1, 2713.1 cm-1. This is because Mode 2 and Mode 3 are degenerate, Mode 5 and Mode 6 are degenerate. Mode 4 (2580 cm-1) is not shown in the spectrum since all the dipole moments cancelled out with each other hence it's IR inactive.

==== The MO Diagram of BH3 ====

[[File:LY_BH3_MOs.PNG|The MO diagram of BH3 molecule]]

'''Q1. Are there any significant differences between the real and LCAO MOs?'''

LCAO MOs does not provide an actual description of the molecular orbitals but an optimised and predicted one, forming by each of the AOs, which can be used as reference of the real MOs. As it can be seen from the previous MOs diagram, real MOs have the exact sizes of orbitals, and the shape of orbitals and their overlap are shown clearly.

'''Q2. What does this say about the accuracy and usefulness of qualitative MO theory?'''

The accuracy of the qualitative MO is not as high as the real MOs but it is a reliable prediction of the real MO hence is quite useful.

----

=== NH3 ===

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

[[File:LY_NH3_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES
</pre>

Thr total energy = -56.55776872 a.u.

'''Jmol image of NH3:'''
<jmol><jmolApplet>
<title>NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of NH3 ====

[[File:LY_NH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -8.5646 -8.5588 -0.0047 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

Frequency analysis file: [[Meida:LY_NH3_FREQ.LOG]]

----

=== NH3BH3 ===

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

[[File:LY_NH3BH3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000122 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000543 0.001800 YES
RMS Displacement 0.000297 0.001200 YES
</pre>

The total energy = -83.22468900 a.u.

'''Jmol image of NH3BH3:'''
<jmol><jmolApplet>
<title>NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency analysis of NH3BH3 ====

[[File:LY_NH3BH3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0009 0.0012 0.0013 14.2356 21.2737 40.8153
Low frequencies --- 266.3131 632.1811 639.4214
</pre>

Frequency analysis file: [[Media:LY_NH3BH3_FREQ.LOG]]

----

=== Association Energy ===

E(BH3) = -26.61532350 a.u.

E(NH3) = -56.55776872 a.u.

E(NH3BH3) = -83.22468900 a.u.

ΔE = E(NH3BH3) - [E(BH3) + E(NH3)] = -83.22468900 - [-26.61532350 - 56.55776872] = -0.05159578 a.u. = -135.47 kJ/mol

'''Q1. Based on your energy calculation is the B-N dative bond weak, medium or strong? What comparison have you made to come to this conclusion?'''

B-N dative bond is weak, comparing to the bond energy of the bonds between Boron and other atoms, such as B-O (536 kJ/mol) and B-F (613 kJ/mol). Comparing to the covalent B-N bond's bond energy 378 kJ/mol, the dative bond is still weak, due to lower electron density in the bond.

----

=== NI3 ===

==== B3LYP/GEN ====

[[File:LY_NI3_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000061 0.000450 YES
RMS Force 0.000037 0.000300 YES
Maximum Displacement 0.000317 0.001800 YES
RMS Displacement 0.000235 0.001200 YES
</pre>

The total energy = -88.80867700 a.u.

'''Jmol image of NI3:'''
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of NI3 ====

[[File:LY_NI3_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -22.8019 -22.7986 -19.9756 -0.0037 0.0040 0.0246
Low frequencies --- 101.7251 101.7253 153.3744
</pre>

Frequency analysis file: [[Media:LY_NI3_FREQ.LOG]]

==== Optimised Bond Distance ====

The optimised bond distance between N-I = 2.184 Å

== Mini Project: Ionic Liquids ==

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

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

[[File:N(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000069 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000752 0.001800 YES
RMS Displacement 0.000236 0.001200 YES
</pre>

The total energy = -214.18127397 a.u.

'''Jmol image of [N(CH3)4]+:'''
<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_N(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequencies Analysis of [N(CH3)4]+ ====

[[File:LY_N(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- -0.0009 -0.0006 -0.0003 22.9947 22.9947 22.9947
Low frequencies --- 189.2288 293.0077 293.0077
</pre>

Frequencies analysis file: [[Media:LY_N(CH3)4_FREQ.LOG]]

----

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

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

[[File:P(CH3)4_631_OPT_SUM.PNG]]

<pre>
Item Value Threshold Converged?
Maximum Force 0.000133 0.000450 YES
RMS Force 0.000033 0.000300 YES
Maximum Displacement 0.000822 0.001800 YES
RMS Displacement 0.000346 0.001200 YES
</pre>

The total energy = -500.82701155 a.u.

'''Jmol image of [P(CH3)4]+:'''
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>LY_P(CH3)4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==== Frequency Analysis of [P(CH3)4]+ ====

[[File:LY_P(CH3)4_FREQ_SUM.PNG]]

<pre>
Low frequencies --- 0.0016 0.0017 0.0028 26.3395 26.3395 26.3395
Low frequencies --- 161.0408 195.5274 195.5274
</pre>

Frequency analysis file: [[Media:LY_P(CH3)4_FREQ.LOG]]

==== Charge Distribution ====

[[File:LY_P(CH3)4_CHARGE.PNG|thumb|The charge distribution of [P(CH3)4]+]]

File:LY P(CH3)4 CHARGE.PNG

2019-05-16T15:40:47Z

Ly617: