ChemWiki - User contributions [en]

Rep:Mod:jc6116

2019-05-24T16:09:17Z

Jc6116: /* Comparison of Charge Distribution */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on each H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H each (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.3

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The total charge are conserved to +1 for both ionic molecule

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:06:32Z

Jc6116: /* JSOML */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:06:01Z

Jc6116: /* JSOML */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>[P(CH3)4]+</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:05:21Z

Jc6116: /* JSOML */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>[N(CH3)4]+</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:05:02Z

Jc6116: /* JSOML */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:04:31Z

Jc6116: /* [N(CH3)4]+ */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:04:05Z

Jc6116: /* Reference */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.

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

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

Rep:Mod:jc6116

2019-05-24T16:03:33Z

Jc6116: /* Item Table of NH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3BH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:03:16Z

Jc6116: /* Item Table */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table of NH3===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:02:39Z

Jc6116: /* Summary Table of NH3BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:02:20Z

Jc6116: /* Low frequency of NH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:02:13Z

Jc6116: /* Item table of NH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:02:05Z

Jc6116: /* Summary Table of NH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:01:52Z

Jc6116: /* basis set of NH3 and NH3BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:01:20Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:01:13Z

Jc6116: /* Vibrational spectrum of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:01:02Z

Jc6116: /* Item Table */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T16:00:24Z

Jc6116: /* Comparison of Charge Distribution */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms3.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:59:32Z

Jc6116: /* Mini Project : Ionic Liquids */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:59:09Z

Jc6116: /* Low frequency */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:58:55Z

Jc6116: /* basis set */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:57:59Z

Jc6116: /* basis set */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log| NI3 Optimizaiton log file]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:57:14Z

Jc6116: /* Association energies */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol) 2.

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:56:22Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:55:40Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

Both of the diagrams give the similar results. the LACO MO is not gives very accurate MOs.
In comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule.

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

The accuracy of the LACO MO is not as high as the real MOs simulation but it is a reliable prediction of the real MOs in small molecule. In addition, the LCAO MOs can be used in prediction of small molecule but for more complex molecule. It will not be that useful.

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:49:39Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

in comparison to the real MOs and LCAO MOs, it can be confirmed that the method of LCAO can be used into the prediction of the MOs of Molecule. Both of the diagrams give the similar results.

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:39:50Z

Jc6116: /* Reference */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Hunt P. Lecture_4_Tut_MO_diagram_BH3. Inorganic Lecture Course. London: Imperial College London; 2019.
2.Yu-Ran Luo and Jin-Pei Cheng "Bond Dissociation Energies" in CRC Handbook of Chemistry and Physics, 96th Edition.

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

Rep:Mod:jc6116

2019-05-24T15:39:11Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals. 1]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:37:21Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|thumb|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:37:06Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|600px|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:36:51Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb| 600px|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:36:40Z

Jc6116:

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb| 600px|left|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:35:53Z

Jc6116:

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb| 600px|left|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:35:35Z

Jc6116: /* BH3 Molecule */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb| 600px|left|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:35:02Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb| 600px|left|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:34:51Z

Jc6116: /* LCAO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb| 600px|left|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:34:26Z

Jc6116: /* LACO MO of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LCAO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG|thumb|left|'''Figure 3.'''The MO diagram for BH3. The 'real' orbitals are placed next to their corresponding linear combination of atomic orbitals (LCAO).]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:28:43Z

Jc6116: /* Vibrational spectrum of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:27:38Z

Jc6116: /* Vibrational spectrum of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|1213
|14
|E'
|very slight
|in-plane bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:26:57Z

Jc6116: /* Vibrational spectrum of BH3 */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|96
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|-
|2716
|125
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T15:12:36Z

Jc6116: /* Visualisation of [N(CH3)4]+ MOs */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

[[File:Jc6116_day4_MO10.PNG]]

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

[[File:Jc6116_day4_MO18.PNG]]

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

[[File:Jc6116_day4_MO19.PNG]]

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

File:Jc6116 day4 MO10.PNG

2019-05-24T15:11:36Z

Jc6116:

File:Jc6116 day4 MO18.PNG

2019-05-24T15:11:28Z

Jc6116:

File:Jc6116 day4 MO19.PNG

2019-05-24T15:11:15Z

Jc6116:

Rep:Mod:jc6116

2019-05-24T14:52:17Z

Jc6116: /* Reference= */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''==
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T14:51:53Z

Jc6116: /* Visualisation of [N(CH3)4]+ MOs */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbitals and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the three H s-orbitals and slight anti-bonding effect through space between three H s-orbitals. After hybridisation, the p-orbital
like ligand orbital have Strong anti-bonding effect with the N p-orbital and slight anti-bonding effect through space.

=='''Reference'''===
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T14:47:06Z

Jc6116: /* Visualisation of [N(CH3)4]+ MOs */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbital and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have anti-bonding effect through space with each other. The MO 18 are likely be the anti bonding orbital. It does not overlap with N atom.

In MO 19, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbital and slight anti-bonding effect through space between two H s-orbital

=='''Reference'''===
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T14:45:27Z

Jc6116: /* Visualisation of [N(CH3)4]+ MOs */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at N s-orbital with the ligands. The Mo 10 are Bonding orbital.

In MO 18, in the methyl group there are strong bonding effect between p-orbital of carbon and the two H s-orbital and slight anti-bonding effect through space between two H s-orbital. After hybridisation, the p-orbital
like ligand orbital have some anti-bonding effect through space with each other. The MO 18 are Most

In MO 19, in the methyl group

=='''Reference'''===
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T14:31:01Z

Jc6116: /* Visualisation of [N(CH3)4]+ MOs */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

<jmol><jmolApplet>
<title>[N(CH3)4]+ molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_NCH4_FRE1.LOG</uploadedFileContents>
</jmolApplet></jmol>

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

<jmol><jmolApplet>
<title>NI3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY3_PCH4_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

The Anti-bonding character increasing from MO 10 to MO 19.

In MO 10, all methyl groups are have strong bonding character and anti-bonding only take place at C s-orbital

In MO 18,

=='''Reference'''===
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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

Rep:Mod:jc6116

2019-05-24T14:08:53Z

Jc6116: /* Comparison of Charge Distribution */

== '''BH3 Molecule''' ==

==='''Basis Set'''===
B3LYP/6-31G(d.p.)

==='''Summary Table'''===
[[File:jc6116_day1_bh3_summary.PNG]]

==='''Item Table'''===

Item Value Threshold Converged?
Maximum Force 0.000004 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000017 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

<jmol><jmolApplet>
<title>BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_BH3_2_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

==='''Frequency Analysis'''===
Low frequencies --- -11.6892 -11.6814 -6.5475 0.0011 0.0281 0.4290
Low frequencies --- 1162.9746 1213.1390 1213.1392

==='''Frequency Link'''===

[[Media:JC6116_DAY1_BH3_2_FRE.LOG]]

==='''Vibrational spectrum of BH3'''===

{| class="wikitable"
|+
|-
|wavenumber (cm-1) || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2"
|yes
|out-of-plane bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|1213
|14
|E'
|very slight
|bend
|-
|2582
|0
|A1'
|no
|symmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|-
|2716
|126
|E'
|yes
|asymmetric stretch
|}

[[File:Jc6116_day1_bh3_ir.PNG]]

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

==='''LACO MO of BH3'''===

[[File:Jc6116_day1_BH3_LACO.PNG]]

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

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

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

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

=='''Association energies: Ammonia-Borane'''==

===basis set of NH3 and NH3BH3===

B3LYP/6-31G(d.p.)

===Summary Table of NH3===

[[File:Jc6116_day1_NH3.PNG]]

===Item table of NH3===
Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000016 0.001800 YES
RMS Displacement 0.000011 0.001200 YES

===Low frequency of NH3===

Low frequencies --- -0.0138 -0.0032 -0.0015 7.0783 8.0932 8.0937
Low frequencies --- 1089.3840 1693.9368 1693.9368

[[Media:JC6116_DAY1_NH3_FRE.LOG| NH3 frequency Link ]]

<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_DAY1_NH3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Summary Table of NH3BH3===

[[File:Jc6116_NH3BH3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000123 0.000450 YES
RMS Force 0.000058 0.000300 YES
Maximum Displacement 0.000515 0.001800 YES
RMS Displacement 0.000296 0.001200 YES

===Low Frequency of NH3BH3===

Low frequencies --- -0.0254 -0.0034 -0.0012 17.0395 17.0420 36.9083
Low frequencies --- 265.7476 632.2122 639.3355

[[Media:JC6116_NH3BH3_3_FRE.LOG| NH3BH3 frequency Link]]

<jmol><jmolApplet>
<title>NH3BH3 molecule</title>
<color>black</color>
<size>300</size>
<uploadedFileContents>JC6116_NH3BH3_3_FRE.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Association energies===

E(NH3)= -56.55776872 a.u.
E(BH3)=-26.61532364 a.u.
E(NH3BH3)= -83.22468864 a.u.

ΔE=E(NH3BH3)-[E(NH3)+E(BH3)]
=-0.05159631 a.u.
=-135.4660523 kJ/mol
= ca. -135.47 kJ/mol

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

The dative bond of the B-N is reality weak (135 KJ/mol) compare with the C-C (346 KJ/mol) bond B-H bond (345 kJ/mol).

=='''PPs and NI3'''==

===basis set===

[[Media:Log_10056936.log]]

===Summary Table===

[[File:Jc6116_NI3_2_sum.PNG]]

===Item Table===

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000493 0.001800 YES
RMS Displacement 0.000333 0.001200 YES

===Low frequency ===

Low frequencies --- -12.7380 -12.7319 -6.2907 -0.0040 0.0188 0.0633
Low frequencies --- 101.0326 101.0333 147.4124

[[Media:JC6116_NH3BH3_2_FRE.LOG| NI3 frequency Link]]

<jmol><jmolApplet>
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===Bond Length===
The Optimized bond distance is 2.184Å

=='''Mini Project : Ionic Liquids'''==

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

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

[[File:Jc6116_day3_NCH4_FRE_sum.PNG]]

===== Item Table=====

Item Value Threshold Converged?
Maximum Force 0.000068 0.000450 YES
RMS Force 0.000017 0.000300 YES
Maximum Displacement 0.000922 0.001800 YES
RMS Displacement 0.000282 0.001200 YES

===== Low Frequency=====

Low frequencies --- -0.0004 0.0004 0.0009 22.4056 22.4056 22.4057
Low frequencies --- 188.7251 292.7157 292.7157

[[Media:JC6116_DAY3_NCH4_FRE1.LOG]]

=====JSOML=====

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

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

====Summary Table====

[[File:jc6116_day3_PCH4_sum.PNG]]

====Item Table====

Item Value Threshold Converged?
Maximum Force 0.000128 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000666 0.001800 YES
RMS Displacement 0.000277 0.001200 YES

====Low Frequency====

Low frequencies --- 0.0006 0.0015 0.0029 26.3157 26.3157 26.3157
Low frequencies --- 160.9744 195.4740 195.4740

[[Media:JC6116_DAY3_PCH4_FRE.LOG]]

====JSOML====

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===Comparison of Charge Distribution===

[[File: Jc6116_day3_PCH4_chr.PNG |thumb | Charge Distribution of PCH4 |500px| left]]

[[File: Jc6116_day3_NCH4_chr.PNG |400px|thumb| Charge Distribution of NCH4 |center]]

Real Charge Distribution on Molecule
[N(CH3)4]+ N:-0.295 C: -0.483 H: +0.269
[P(CH3)4]+ P:+1.667 C: -1.252 H: +0.298

In the transitional formal charge assignment Both ionic molecules [N(CH3)4]+ and [P(CH3)4]+ have +1 charge and the centre atom N and P have +1 charge. However, in the real situation, in [N(CH3)4]+, all the positive charge sit on H atoms (+0.269), while in [P(CH3)4]+ positive charge spread on both H (+0.298) and P (+1.667) atoms. This result can be explained by the electronegativity difference between atoms.

In [P(CH3)4]+, C is the most electronegative atom while P and H have nearly the same electronegativity.(P: 2.1, H: 2.1, C: 2.5). Thus, the electron densities on the H and P atoms are pulled toward C atoms

In [N(CH3)4]+, N is the most electronegative atom (N: 3.0, C: 2.5, H: 2.1), therefore positive charge are all on H atoms.

The Charge distribution are symmetrical through all space because the dipole moment are zero for both ionic molecules.

===Visualisation of [N(CH3)4]+ MOs===

{| class="wikitable" border=1
! MO !! Real MOs !! LCAO MOs !! Ligand FO !! Occupied?
|-
| MO = 10 || [[File:Jc6116_day3_MO10.PNG]] || [[File:Jc6116_day3_MO10_3.PNG]] || s-orbital of C, s-orbitals of 3 H || Yes
|-
| MO = 18 || [[File:Jc6116_day3_MO18.PNG]] || [[File:Jc6116_day3_MO18_1.PNG]] || p-orbital of C, s-orbitals of 2 H || Yes
|-
| MO = 19 || [[File:Jc6116_day3_MO19.PNG]] || [[File:Jc6116_day3_MO19_1.PNG]] || p-orbital of C, s-orbitals of 3 H || Yes
|}

=='''Reference'''===
1.Figure 5 on Lecture_4_Tut_MO_diagram_BH3 sheet, Prof. Patricia Hunt

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

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