==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317hfbh3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised BH3====
<jmol><jmolApplet>
<title>Optimised BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_SYM_OPT_D3H.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 B3LYP/3-21G level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SIM_NH3BH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Low frequencies====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:simrankaurgill.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NI3_631G_PP_BASISSETSG2317.LOG</uploadedFileContents>
</jmolApplet></jmol>

Optimised N-I distance is 2.18396

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

====Jmol image====

<jmol><jmolApplet>
<title>Optimised N+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_N+_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

====Jmol image====
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_P+_631G_TD_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

File:Simrankaurgill.png

2019-05-24T16:33:35Z

Sg2317:

Sg2317hf

2019-05-24T16:33:08Z

Sg2317: /* Summary */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317hfbh3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised BH3====
<jmol><jmolApplet>
<title>Optimised BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_SYM_OPT_D3H.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 B3LYP/3-21G level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SIM_NH3BH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Low frequencies====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:simrankaurgill.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NI3_631G_PP_BASISSETSG2317.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

====Jmol image====

<jmol><jmolApplet>
<title>Optimised N+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_N+_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

====Jmol image====
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_P+_631G_TD_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T16:29:31Z

Sg2317: /* What is your optimised N-I distance? */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317hfbh3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised BH3====
<jmol><jmolApplet>
<title>Optimised BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_SYM_OPT_D3H.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 B3LYP/3-21G level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SIM_NH3BH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Low frequencies====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NI3_631G_PP_BASISSETSG2317.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

====Jmol image====

<jmol><jmolApplet>
<title>Optimised N+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_N+_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

====Jmol image====
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_P+_631G_TD_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

2019-05-24T16:11:52Z

Sg2317: /* Link to log file */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised BH3====
<jmol><jmolApplet>
<title>Optimised BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_SYM_OPT_D3H.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SIM_NH3BH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NI3_631G_PP_BASISSETSG2317.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

====Jmol image====

<jmol><jmolApplet>
<title>Optimised N+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_N+_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

====Jmol image====
<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_P+_631G_TD_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

File:SG2317 P+ 631G TD FREQ.LOG

2019-05-24T16:08:58Z

Sg2317:

Sg2317hf

2019-05-24T16:07:27Z

Sg2317: /* jmol image */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised BH3====
<jmol><jmolApplet>
<title>Optimised BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_SYM_OPT_D3H.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NH3BH3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SIM_NH3BH3_631G_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>Optimised NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_NI3_631G_PP_BASISSETSG2317.LOG</uploadedFileContents>
</jmolApplet></jmol>

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

====Jmol image====

<jmol><jmolApplet>
<title>Optimised N+</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_N+_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T16:07:09Z

Sg2317hf

2019-05-24T15:52:56Z

Sg2317: /* Jmol image of optimised NI3 */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised BH3====
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_SYM_OPT_D3H.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

File:SG2317 BH3 SYM OPT D3H.LOG

2019-05-24T15:52:08Z

Sg2317:

File:SG2317 BH3 OPT.LOG

2019-05-24T15:50:07Z

Sg2317: Sg2317 uploaded a new version of File:SG2317 BH3 OPT.LOG

Sg2317hf

2019-05-24T15:47:13Z

Sg2317: /* Section of file */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3_631G_pp_BASISSETSG2317.log</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Low frequencies====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T15:46:50Z

Sg2317: /* Vibrational spectrum for NH3 */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3_631G_pp_BASISSETSG2317.log</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Section of file====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155
Diagonal vibrational polarizability:
0.7185611 0.7184609 1.8403802
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1163.1897 1213.3128 1213.3155
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9989 0.9603 0.9603
IR Inten -- 92.5285 14.0641 14.0677
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for BH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T15:46:10Z

Sg2317: /* Link to jmol file */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3_631G_pp_BASISSETSG2317.log</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Section of file====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155
Diagonal vibrational polarizability:
0.7185611 0.7184609 1.8403802
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1163.1897 1213.3128 1213.3155
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9989 0.9603 0.9603
IR Inten -- 92.5285 14.0641 14.0677
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_opt_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for NH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

File:SG2317 BH3 OPT 1.LOG

2019-05-24T15:45:15Z

Sg2317:

Sg2317hf

2019-05-24T15:42:43Z

Sg2317: /* Link to log file */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3_631G_pp_BASISSETSG2317.log</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Section of file====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155
Diagonal vibrational polarizability:
0.7185611 0.7184609 1.8403802
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1163.1897 1213.3128 1213.3155
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9989 0.9603 0.9603
IR Inten -- 92.5285 14.0641 14.0677
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====Link to jmol file====
<jmol><jmolApplet>
<title>SG2317_BH3_OPT_1</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>SG2317_BH3_OPT_1.log</uploadedFileContents>
</jmolApplet></jmol>

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for NH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T15:37:10Z

Sg2317: /* Jmol image of optimised NI3 */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====
<jmol><jmolApplet>
<title>NI3</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>NI3_631G_pp_BASISSETSG2317.log</uploadedFileContents>
</jmolApplet></jmol>

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Section of file====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155
Diagonal vibrational polarizability:
0.7185611 0.7184609 1.8403802
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1163.1897 1213.3128 1213.3155
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9989 0.9603 0.9603
IR Inten -- 92.5285 14.0641 14.0677
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for NH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T15:33:22Z

Sg2317: /* MO 18 */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Section of file====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155
Diagonal vibrational polarizability:
0.7185611 0.7184609 1.8403802
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1163.1897 1213.3128 1213.3155
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9989 0.9603 0.9603
IR Inten -- 92.5285 14.0641 14.0677
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for NH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

====Comments====

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.

Sg2317hf

2019-05-24T15:32:57Z

Sg2317: /* MO 18 */

==BH3 optimisation==

===BH3: B3LYP/3-21G level===

====Summary====
[[File:sg2317_bh3_3.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000090 0.000450 YES
RMS Force 0.000059 0.000300 YES
Maximum Displacement 0.000351 0.001800 YES
RMS Displacement 0.000230 0.001200 YES
Predicted change in Energy=-4.723230D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_opt_1.log| here]]

===BH3 optimisation: 6-31G(d,p) level===

====Summary====
[[File:sg2317bh3bettersummary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000203 0.000450 YES
RMS Force 0.000098 0.000300 YES
Maximum Displacement 0.000737 0.001800 YES
RMS Displacement 0.000395 0.001200 YES
Predicted change in Energy=-1.355408D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_OPT.log| here]]

====Jmol image of optimised NI3====

===BH3 with D3h symmetry===
[[File:sg2317bh3d3h.png|300px]]

===BH3 frequency analysis===
[[File:sg2317bh3freqopt.png|300px]]

====Item section of file====
Item Value Threshold Converged?
Maximum Force 0.000046 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.000182 0.001800 YES
RMS Displacement 0.000091 0.001200 YES
Predicted change in Energy=-1.259145D-08
Optimization completed.

====Section of file====
Low frequencies --- -0.4072 -0.1962 -0.0055 25.2514 27.2430 27.2460
Low frequencies --- 1163.1897 1213.3128 1213.3155
Diagonal vibrational polarizability:
0.7185611 0.7184609 1.8403802
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2" E' E'
Frequencies -- 1163.1897 1213.3128 1213.3155
Red. masses -- 1.2531 1.1072 1.1072
Frc consts -- 0.9989 0.9603 0.9603
IR Inten -- 92.5285 14.0641 14.0677
Atom AN X Y Z X Y Z X Y Z
1 5 0.00 0.00 0.16 0.00 0.10 0.00 -0.10 0.00 0.00
2 1 0.00 0.00 -0.57 0.00 0.08 0.00 0.81 0.00 0.00
3 1 0.00 0.00 -0.57 -0.39 -0.59 0.00 0.14 0.39 0.00
4 1 0.00 0.00 -0.57 0.39 -0.59 0.00 0.14 -0.39 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_BH3_SYNSIM_OPY.log| here]]

====IR spectrum or BH3====
[[File:sg2317_bh3_ir.png|500px]]

=====Vibrational spectrum for NH3=====

{| class="wikitable"
|+
|-
|Wavenumber (cm-1 || Intensity (arbitrary units) || Symmetry || IR active? || Type
|-
|1163
|92
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|1213
|14
|E'
|slight
|in-plane bend
|-
|2582
|0
|A'1
|no
|totally symmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|-
|2714
|126
|E'
|yes
|asymmetric stretch
|}

===BH3 MO analysis===
[[File:SIM_MO.png]]
<ref name="Hunt MO BH3" />
<references>
<ref name="Hunt MO BH3">This is the MO diagram for BH3 taken from Dr Hunt's handout. http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf</ref>
</references>

====Are there significant differences between the real and LCAO MOs?====
In real MOs, molecular orbitals are delocalised throughout the whole molecule; whereas in the diagram above using LCAOs the orbitals are shown as individual contributions from each atom of B or H as localised molecular orbitals (aka canonical molecular orbitals). The LCAO orbitals also represent regions in a molecule where an electron occupying that orbital is to be found, however in reality the electron may not be there.
<ref name="Wiki info MO" />
<references>
<ref name="Wiki info MO">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital</ref>
</references>

====What does this say about the accuracy and usefulness of qualitative MO theory?====
The molecular orbital wave function can be written as a weighted sum of each atomic orbital. Using:
[[File:eqsg2317.png]]

The coefficients can be determined by substituting the sum into the Schrodinger equation and applying the variational principle. This quantifies the orbital contribution.

Overall, MO diagram can be used to make an accurate prediction for solutions to the Schrodinger equation.
<ref name="Wiki info MO theory" />
<references>
<ref name="Wiki info MO theory">Information cited from https://en.wikipedia.org/wiki/Molecular_orbital_theory</ref>
</references>

==NH3 optimisation==

===NH3 (3-21G) level===

====Summary====
[[File:sim_nh3_opt_321g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000057 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000145 0.001800 YES
RMS Displacement 0.000096 0.001200 YES
Predicted change in Energy=-1.132410D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_321g_optimisation.log| here]]

===NH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_opt_631g.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000058 0.000450 YES
RMS Force 0.000039 0.000300 YES
Maximum Displacement 0.000370 0.001800 YES
RMS Displacement 0.000162 0.001200 YES
Predicted change in Energy=-2.215151D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_optimisation.log| here]]

===NH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000099 0.000450 YES
RMS Force 0.000041 0.000300 YES
Maximum Displacement 0.000342 0.001800 YES
RMS Displacement 0.000114 0.001200 YES
Predicted change in Energy=-2.170625D-08
Optimization completed.

====Section of file====
Low frequencies --- -32.8801 -32.8674 -11.9107 -0.0036 0.0074 0.0513
Low frequencies --- 1088.6732 1694.0154 1694.0157
Diagonal vibrational polarizability:
0.1278779 0.1278790 3.3103610
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A1 E E
Frequencies -- 1088.6732 1694.0154 1694.0157
Red. masses -- 1.1800 1.0645 1.0645
Frc consts -- 0.8240 1.7998 1.7998
IR Inten -- 145.6893 13.5777 13.5779
Atom AN X Y Z X Y Z X Y Z
1 7 0.00 0.00 0.12 -0.07 0.00 0.00 0.00 0.07 0.00
2 1 0.00 -0.21 -0.53 0.76 0.00 0.00 0.00 0.15 0.26
3 1 0.18 0.11 -0.53 0.08 -0.39 0.22 0.39 -0.53 -0.13
4 1 -0.18 0.11 -0.53 0.08 0.39 -0.22 -0.39 -0.53 -0.13

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3_631g_freq.log| here]]

==NH3BH3 optimisation==

===NH3BH3 B3LYP/(3-21G) level===

====Summary====
[[File:sim_nh3bh3_321g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000094 0.000450 YES
RMS Force 0.000030 0.000300 YES
Maximum Displacement 0.000419 0.001800 YES
RMS Displacement 0.000179 0.001200 YES
Predicted change in Energy=-5.743893D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_321g.log| here]]

===NH3BH3 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000137 0.000450 YES
RMS Force 0.000038 0.000300 YES
Maximum Displacement 0.000989 0.001800 YES
RMS Displacement 0.000393 0.001200 YES
Predicted change in Energy=-1.212361D-07
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_nh3bh3_631g.log| here]]

===NH3BH3 Frequency and MOs: 6-31G(d,p) level===

====Summary====
[[File:sim_nh3bh3_631g_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000260 0.000450 YES
RMS Force 0.000057 0.000300 YES
Maximum Displacement 0.001414 0.001800 YES
RMS Displacement 0.000342 0.001200 YES
Predicted change in Energy=-2.014452D-07
Optimization completed.

====Section of file====
Low frequencies --- -0.1676 -0.0620 -0.0067 12.6988 16.2670 16.2765
Low frequencies --- 263.1439 631.3651 638.8717
Diagonal vibrational polarizability:
2.5456848 2.5457021 5.0369316
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1 2 3
A2 A1 E
Frequencies -- 263.1291 631.3651 638.8715
Red. masses -- 1.0078 5.0032 1.0452
Frc consts -- 0.0411 1.1751 0.2513
IR Inten -- 0.0000 14.1193 3.5559
Atom AN X Y Z X Y Z X Y Z
1 1 -0.45 0.00 0.00 0.00 0.00 0.36 0.00 -0.17 0.59
2 1 0.22 -0.39 0.00 0.00 0.00 0.36 0.02 -0.20 -0.29
3 1 0.22 0.39 0.00 0.00 0.00 0.36 -0.02 -0.20 -0.29
4 1 -0.36 0.00 0.00 0.00 -0.03 -0.29 0.00 -0.11 0.46
5 1 0.18 0.32 0.00 -0.03 0.02 -0.29 -0.02 -0.14 -0.23
6 1 0.18 -0.32 0.00 0.03 0.02 -0.29 0.02 -0.14 -0.23
7 7 0.00 0.00 0.00 0.00 0.00 0.36 0.00 0.05 0.00
8 5 0.00 0.00 0.00 0.00 0.00 -0.48 0.00 0.03 0.00

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NH3BH3_631g_freq.log| here]]

====Include a Jmol image of your optimised geometry in your wiki====

====What is your optimised N-I distance?====
2.18363 au <- check units here

==Association energies calculations==

{| class="wikitable"
|+
|-
|Molecule || Energy (arbitrary units)
|-
|NH3 || -56.6
|-
|BH3 || -26.6
|-
|NH3BH3 || -83.2
|-
|}

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]

ΔE=(-83.22469010) - [(-56.55776860)+(-26.61532362)]

ΔE= -0.05159788 au

ΔE= -134 kJ/mol

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

It's a weak bond. The bond enthalpy to Al-N is 297 kJ/mol; it takes 163 kJ/mol less energy to break the B-N bond.
The bond is made as a result of electron donation from the Nitrogen lone pair into the empty orbital of B. This is a dative covalent bond.
The B-N bond is weaker than Al-N; this may be because the orbitals are more diffuse in Al as it is one period below B. As a result there is more efficient orbital overlap and a stronger bond.
<ref name="Bond enthalpy data" />
<references>
<ref name="Bond enthalpy data">Information cited from https://labs.chem.ucsb.edu/zakarian/armen/11---bonddissociationenergy.pdf</ref>
</references>

==NI3==

====Summary====

[[File:sg2317_NI3_ppbs_summary.png|300px]]

====Item section of output====

Item Value Threshold Converged?
Maximum Force 0.000066 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000480 0.001800 YES
RMS Displacement 0.000327 0.001200 YES
Predicted change in Energy=-5.608968D-08
Optimization completed.

====Section of file====
ASK EUAN AB ADDING LOW FREQUENCY LINES HERE

====Link to log file====
The optimisation file is linked to [[Media:SG2317_NI3_631G_PP_BASISSETsg2317.log| here]]

==Ionic liquids, designer solvents==

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

====Summary====

[[File:sim_n+_opt_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000020 0.000450 YES
RMS Force 0.000008 0.000300 YES
Maximum Displacement 0.000056 0.001800 YES
RMS Displacement 0.000025 0.001200 YES
Predicted change in Energy=-7.411317D-09
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt.log| here]]

====Summary for frequency====

[[File:sg2317_n+_opt_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000097 0.000450 YES
RMS Force 0.000049 0.000300 YES
Maximum Displacement 0.000882 0.001800 YES
RMS Displacement 0.000487 0.001200 YES
Predicted change in Energy=-4.705137D-07
Optimization completed.

====Low frequency====
Low frequencies --- 0.0007 0.0007 0.0007 34.8305 34.8305 34.8305
Low frequencies --- 217.4553 316.5611 316.5611

====Link to log file====
The optimisation file is linked to [[Media:sim_n+_opt_freq.log| here]]

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

====Summary====

[[File:sg2317_p+_631g_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000034 0.000450 YES
RMS Force 0.000014 0.000300 YES
Maximum Displacement 0.000157 0.001800 YES
RMS Displacement 0.000071 0.001200 YES
Predicted change in Energy=-3.029697D-08
Optimization completed.

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td.log| here]]

====Summary for frequency====
[[File:sg2317_p+_631g_td_freq_summary.png|300px]]

====Item section of output====
Item Value Threshold Converged?
Maximum Force 0.000186 0.000450 YES
RMS Force 0.000107 0.000300 YES
Maximum Displacement 0.001331 0.001800 YES
RMS Displacement 0.000800 0.001200 YES
Predicted change in Energy=-1.314624D-06
Optimization completed.

====Low frequency====
Low frequencies --- -0.0034 -0.0031 -0.0026 50.7931 50.7931 50.7931
Low frequencies --- 187.1415 211.9878 211.9878

====Link to log file====
The optimisation file is linked to [[Media:sg2317_p+_631g_td_freq.log| here]]

==Charge distribution analysis for [N(CH3)4]+ and [P(CH3)4]+==
[[File:sg2317_n+_charge.png|300px|left|thumb|A charge distribution of [N(CH3)4]+ by colour]] [[File:sg2317_p+_charge.png|300px|left|thumb|A charge distribution of [P(CH3)4]+ by colour]]

===Charge on atoms===

{| class="wikitable"
|+
|-
|Atom(s) || Charge in [P(CH3)4]+ || Charge in [N(CH3)4]+
|-
|Heteroatom || 1.667 || -0.295
|-
|C || -1.060 || -0.483
|-
|H|| 0.298 || 0.269
|-
|}

===Discussion===
In the charge analysis, the colour range was set from -1.7 to 1.7 for both atoms. This allows a more accurate comparison to be made.
Although, it could be predicted that the molecules would have a similar charge distribution as they are similar in structure this is not the case.

Description:
In [N(CH3)4]+, the charges are more delocalised; the H atoms have a positive charge and the heteroatom (N) and the C atoms have negative charges, with C being more negatively charged.
But, in the [P(CH3)4]+, only the C atoms have negative charges, of which are significantly more negative than in [N(CH3)4]+, and the heteroatom (P) and the H atoms have positive charges. The P is very interesting in particular as it has a very positive localised charge.

Heteroatoms:
N and P carry charges of the opposite sign. The N is negative, but the P is positive.
N (3.04) is more electronegative than C (2.55), so you would expect more of a negative charge on the N atoms; however this is not the case because N participates n=in dative bonding and so has less electrons than expected and is "positive". P (2.19) is less electronegative than C (2.55), so there is more of a negative charge on C atoms.
The C-heteroatom bonds are more polarised in [P(CH3)4]+. This is likely to be because N is so electronegative that it doesn't retain positive charge well, so the charges are more delocalised over the molecule.
Because P is one period below N , P orbitals are more diffuse, and the positive charge is more spread over the molecule, this can lead to the negative charges to be lower in magnitude on the C atoms in [P(CH3)4]+ than in [N(CH3)4]+.

Carbon atoms:
In both molecules, the C atoms are negative (less so in [P(CH3)4]+ due to the stabilisation from the positive charge on the P)

Hydrogen atoms:
In both molecules, the H atoms are positive. There isn't significant difference in magnitude of these charges either; this is likely to be because the effect of electronegativity falls with distance.

===Questions to answer===
What does the "formal" positive charge on the N represent in the traditional picture?

If we draw the Lewis structure of [N(CH3)4]+, a positive charge arises. This is because N has 5 valence electrons; 3 of the bonds to methyl groups are due to covalent bonds but, one of the C-N is a dative covalent bond arising from donation of the lone pair on N. There are now less electrons than expected on the N and the positive charge demonstrates this.

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

The positive charge is delocalised over the N and the C.

==Molecular orbitals==

===MO 6===
Here there are bonding interactions between S orbitals on the C atoms in each methyl, each H and the N atom.

[[File:sg2317_MO6_pic.png|300px|left]]

[[File:SIM_MO6_LCAO.png|300px|centre]]

===MO 10===
There are bonding interactions between the s orbitals on the H atoms and the S orbitals of the N atom. And the p orbitals of the C; this is because the nodes cut through the C atoms - this is what happens with p orbitals. There is some anti-bonding character between space; represented by the red and green areas being close.

[[File:sg2317_MO_10.png|300px|left]]

[[File:SIM_MO10_LCAO.png|300px|centre]]

===MO 18===

There is anti-bonding character through space and at each methyl group. The MO is a result of mixing of only 2 of the 3 s orbitals from H on each methyl. They are mixing with p orbitals on C. This can be demonstrated because there are nodes on each C.

[[File:sg2317_MO18.png|300px|left]]

[[File:SIM_MO18_LCAO.png|300px|centre]]

It is interesting how in MO18 only 2 of the H atoms per methyl group have orbitals participating. The 3rd H has no orbitals contributing.
Furthermore, the MO diagram can be constructed with help of the BH3 MO; as the MO from that diagram can be used to help represent each methyl group mixing with the N atom here.