ChemWiki - User contributions [en]

Rep:Mod:Jun Lore

2019-05-23T17:26:31Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
!MO 9

![[File:jun_mo9.PNG|600px]]

![[File:jun_mo9mo.PNG|400px]]
|}

{| class="wikitable"
!MO 16

![[File:jun_mo16.PNG|600px]]

![[File:jun_mo16mo.PNG|400px]]
|}

{| class="wikitable"
!MO 19

![[File:jun_mo19mo.PNG|600px]]

![[File:jun_mo19.PNG|400px]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T17:26:03Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
!MO 9

![[File:jun_mo9.PNG|600px]]

![[File:jun_mo9mo.PNG|400px]]
|}

{| class="wikitable"
![[File:jun_mo16.PNG|600px]]

![[File:jun_mo16mo.PNG|400px]]
|}

{| class="wikitable"
![[File:jun_mo19mo.PNG|600px]]

![[File:jun_mo19.PNG|400px]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T16:22:16Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
![[File:jun_mo9.PNG|600px]]

![[File:jun_mo9mo.PNG|400px]]
|}

{| class="wikitable"
![[File:jun_mo16.PNG|600px]]

![[File:jun_mo16mo.PNG|400px]]
|}

{| class="wikitable"
![[File:jun_mo19mo.PNG|600px]]

![[File:jun_mo19.PNG|400px]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

File:Jun mo19mo.PNG

2019-05-23T16:22:09Z

Hw4717:

File:Jun mo19.PNG

2019-05-23T16:21:57Z

Hw4717:

File:Jun mo16.PNG

2019-05-23T16:21:48Z

Hw4717:

File:Jun mo16mo.PNG

2019-05-23T16:21:39Z

Hw4717:

Rep:Mod:Jun Lore

2019-05-23T16:20:42Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
![[File:jun_mo9.PNG|600px]]

![[File:jun_mo9mo.PNG|400px]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T16:20:27Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
![[File:jun_mo9.PNG|800px]]

![[File:jun_mo9mo.PNG|400px]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T16:20:02Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
![[File:jun_mo9.PNG|500px]]

![[File:jun_mo9mo.PNG|500px]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T16:19:35Z

Hw4717: /* Molecular Orbital Calculations */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===
{| class="wikitable"
![[File:jun_mo9.PNG]]

![[File:jun_mo9mo.PNG]]
|}

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

File:Jun mo9mo.PNG

2019-05-23T16:19:32Z

Hw4717:

File:Jun mo9.PNG

2019-05-23T16:19:14Z

Hw4717:

Rep:Mod:Jun Lore

2019-05-23T14:36:47Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and nitrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T14:34:18Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher 
in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and notrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T14:34:02Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
From the data shown, it can be noticed that in [N(CH3)4]+, N and C atoms carry 
the negative charge and the hydrogen carries the positive charge. That is due to the different 
electronegativity of the atoms, the order of which is N > C > H. Therefore, carbon is the most 
negative atom in the cation which pull the electrons toward themselves and make the hydrogen 
become positive in the cation. N is also electronegative so also carries the negative charge on 
it. For [P(CH3)4]+, the decreasing order of electronegativity is C > P > H. The carbon pulls electrons 
on hydrogens and phosphorus making itself and hydrogens more positive, due to carbon is higher in electronegativity.

Another information can be derived is that there exist a dative N-H bond and a dative P-H bond. 
The lone pair of electrons on nitrogen and phosphorus contribute to the formation of the dative bond. 
From this presentation, the phosphorus shows positive charge because sharing the electrons to the 
hydrogen as well as its lower electronegativity compared to carbon and notrogen. In addition, the 
hydrogen atoms are carrying the positive charge from the calculation in Gaussian.

Rep:Mod:Jun Lore

2019-05-23T13:54:41Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.7 to +1.7
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:54:05Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:53:52Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges (DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>
 

[P(CH3)4]+ charges (DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:53:32Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.30
<li>Hydrogen: 0.27
<li>Carbon: -0.48
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.67
<li>Hydrogen: 0.30
<li>Carbon: -1.06
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:51:34Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:jun_ncharge.PNG|700px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|700px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:51:15Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:jun_ncharge.PNG|500px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:jun_pcharge.PNG|500px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

File:Jun pcharge.PNG

2019-05-23T13:51:11Z

Hw4717:

File:Jun ncharge.PNG

2019-05-23T13:51:01Z

Hw4717:

Rep:Mod:Jun Lore

2019-05-23T13:39:19Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:charge_n.PNG|500px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:charge_p.PNG|500px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:39:05Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:charge_n.PNG|500px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:charge_p.PNG|500px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:38:49Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:charge_n.PNG|500px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:charge_p.PNG|500px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

 
 
 
 
 
 
 
 
The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:25:21Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -1.0 to +0.8
 
[[File:charge_n.PNG|500px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:charge_p.PNG|500px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:22:17Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|500px|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:charge_p.PNG|500px|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:21:17Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|thumb|left|Charge distribution for [N(CH3)4]+]]
 
[[File:charge_p.PNG|thumb|left|Charge distribution for [P(CH3)4]+]]
 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:20:51Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|thumb|left|Charge distribution for [N(CH3)4]+]] 
[[File:charge_p.PNG|thumb|left|Charge distribution for [P(CH3)4]+]] 

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:20:22Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:20:06Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG]]
[[File:charge_p.PNG|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:19:24Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|thumb|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:18:35Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|700px|thumb|center|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|850px|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:18:22Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|700px|thumb|center|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|800px|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:18:09Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|750px|thumb|center|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|800px|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:17:26Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|800px|thumb|center|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|800px|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

Rep:Mod:Jun Lore

2019-05-23T13:17:05Z

Hw4717: /* Charge Distribution Calculation */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
This illustrates the usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 
However, there is still some difference comparing 3a1 and 2e MOs. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>
 

===Molecular Orbital Calculations===

===Charge Distribution Calculation===

A full NBO charge analysis was performed with a range of -0.6 to +0.6
 
[[File:charge_n.PNG|thumb|center|Charge distribution for [N(CH3)4]+]]
[[File:charge_p.PNG|thumb|center|Charge distribution for [P(CH3)4]+]]

[N(CH3)4]+ charges(DEBYE):

<ul>
<li>Nitrogen: -0.295
<li>Hydrogen: 0.269
<li>Carbon: -0.483
</ul>

[P(CH3)4]+ charges(DEBYE):

<ul>
<li>Phosphorous: 1.667
<li>Hydrogen: 0.298
<li>Carbon: -1.060
</ul>

The formal charge on the Nitrogen or Phosphorous is merely a convention, assuming 
that electrons in all chemical bonds are shared equally between atoms, regardless of 
relative electronegativity. It is also assumed that electrons are localised in the bonds 
and thus formal charges in the valence bond model keep track of the electrons around the 
atom, in this case N or P. However, as shown in both molecules the charge is delocalised 
in the entire molecule . 
Specifically in [N(CH3)4]+ the positive charge is found on the electropostive protons, while 
the nitrogen, being an electronegative element is negatively charged. This is the opposite of what 
of what VSEPR and localisation of bonds predict, exactly because in real molecules, molecular 
orbitals that span all over the entire molecule are present, leading to delocalisation of the 
charge. 
When compared to [N(CH3)4]+ , the charge separation in the C-P bond is greater than in the N-P bond 
due to the greater difference in electronegativity between C&P(𐤃elec=0.49) and C&N(𐤃elec=-0.36). Also 
the charge on the phosphorous is now positive since phosphorous is more electropostive than nitrogen. 
Therefore in this case the charge is greatly found on the phosphorous atom and partly in the hydrogens.

File:Charge p.PNG

2019-05-23T13:16:56Z

Hw4717:

File:Charge n.PNG

2019-05-23T13:16:42Z

Hw4717:

Rep:Mod:Jun Lore

2019-05-23T13:13:31Z

Hw4717: /* MINI PROJECT-IONIC LIQUIDS */

Rep:Mod:Jun Lore

2019-05-22T10:03:59Z

Hw4717: /* Molecular orbital calculations */

Rep:Mod:Jun Lore

2019-05-22T10:02:38Z

Hw4717: /* calculation information */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
====calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:Jun Lore

2019-05-22T10:02:09Z

Hw4717: /* Calculation information */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
====Calculation information====
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
===calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:Jun Lore

2019-05-22T10:01:42Z

Hw4717: /* Calculation information */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

====Calculation information====
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
===Calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
===calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:Jun Lore

2019-05-21T16:00:08Z

Hw4717: /* Summary table */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

===Calculation information===
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
===Calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
===calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:Jun Lore

2019-05-21T15:59:51Z

Hw4717: /* Summary table */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

===Calculation information===
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
===Calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
===calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG|350px]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:Jun Lore

2019-05-21T15:59:35Z

Hw4717: /* Summary table */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

===Calculation information===
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
===Calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
===calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG|350px]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG|350px]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

Rep:Mod:Jun Lore

2019-05-21T15:59:22Z

Hw4717: /* Summary table of results */

=Borane (BH3)=
<ul>
<li>BH3 B-H bond length:1.192 Å
<li>BH3 H-B-H bond angle:120.0°
</ul>

===Calculation information===
Frequency file can be found here [[media:JUN_BH3_FREQ.LOG|JUN_BH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000014 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000053 0.001800 YES
RMS Displacement 0.000027 0.001200 YES
Predicted change in Energy=-1.076094D-09
Optimization completed.
-- Stationary point found.
</pre>

====Summary table of results====
[[File:jun_bh3_sum.PNG]]

===Vibrational Information===
====Low frequency lines====
<pre>
Low frequencies --- -7.5936 -1.5614 -0.0054 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

====Rotatable 3d image of optimized BH3====
<jmol><jmolApplet>
<title>BH3 molecule </title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Table of vibrational results====
{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|a) 1163
|93
|A2"
|yes
|out-of-plane bend
|-
|b) 1213
|14
|E'
|very slight
|bend
|-
|c) 1213
|14
|E'
|very slight
|bend
|-
|d) 2582
|0
|A1'
|no
|symmetric stretch
|-
|e) 2716
|126
|E'
|yes
|asymmetric stretch
|-
|f) 2716
|126
|E'
|yes
|asymmetric stretch
|}

====Vibrational spectrum====
 
[[File:jun_bh3_spec.PNG|600px]]
 

Despite the fact that there are 6 vibrations that arise from the calculation, 
only 3 peaks are present. This is due to two reasons. Firstly some of the vibrations 
are double degenerate ( E') and thus they only lead to one peak in the spectrum 
i.e. vibrations b&c (1213.16 cm-1) and vibrations e&f (2715.56 cm-1). Secondly, vibration 
d is not IR active as it is a symmetric stretch that doesn't lead to a change in the 
dipole moment of the molecule. Thus it doesn't appear in the spectrum.

===Molecular orbital calculations===
The molecular orbital diagram for BH3 is illustrated below:
 
[[File:jun_bh3_mo.PNG|650px]]
 ''T.Hunt, 2018, The MO diagram of BH3 - Model answers'' 
''Molecular Orbitals in Inorganic Chemistry, Imperial College London''
 
 
The calculated Molecular Orbitals are in close agreement with the LCAO's diagrams drawn. 
However, there is still some difference comparing 3a1 and 2e MOs. This illustrates the 
usefulness of LCAO's approach and how MO's can be easily and quickly be 
derived from a simple model, with great accuracy without the need of a rigorous calculation. 

=Ammonia (NH3)=
===Calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_NH3_FREQ.LOG|JUN_NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000006 0.000300 YES
Maximum Displacement 0.000039 0.001800 YES
RMS Displacement 0.000013 0.001200 YES
Predicted change in Energy=-3.862150D-10
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -8.5646 -8.5588 -0.0044 0.0454 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865
</pre>

====Summary table of results====
[[File:jun_lore_nh3_sum.PNG]]

====Rotatable 3d image of optimized NH3====
<jmol><jmolApplet>
<title>NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

=NH3BH3=
===calculation information===
Complete optimisation calculations and generated data can be found here [[media:JUN_BH3NH3_FREQ.LOG|JUN_BH3NH3_FREQ.LOG]]

B3LYP/6-31G(d,p)
<pre>
Item Value Threshold Converged?
Maximum Force 0.000372 0.000450 YES
RMS Force 0.000114 0.000300 YES
Maximum Displacement 0.001434 0.001800 YES
RMS Displacement 0.000444 0.001200 YES
Predicted change in Energy=-5.375428D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0674 -0.0572 -0.0066 16.7271 16.7329 41.6572
Low frequencies --- 265.4971 634.5783 640.0015
</pre>

====Summary table====
[[File:jun_bh3nh3_freq_sum_new.PNG|350px]]

====Rotatable 3d image of optimized NH3BH3====
<jmol><jmolApplet>
<title>BH3NH3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_BH3NH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

<ul>
<li>ASSOCIATION ENERGY:
<li>E(NH3) = -56.55777 a.u.
<li>E(BH3) = -26.61532 a.u.
<li>E(NH3BH3) = -83.22469 a.u
<li> ΔE= -83.22469 - (-56.55777 -26.61532) =-0.05160 a.u. or -135.476 kJ/mol
</ul>

Comparing to the typical Carbon-Carbon in an alkyl chain with bond energy 
around 348 kJ/mol and the typical C-N bond of strength 308 kJ/mol, 
the dative covalent bond in BH3NH3 of strength 135 kJ/mol can be considered a weak bond. 

=PP and basis sets for NI3=
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NI3_DSPACE_FREQ.LOG|JUN_NI3_DSPACE_FREQ.LOG]]
 
B3LYP/6-31G(d,p)LANL2DZ NI3
<pre>
Item Value Threshold Converged?
Maximum Force 0.000140 0.000450 YES
RMS Force 0.000092 0.000300 YES
Maximum Displacement 0.001083 0.001800 YES
RMS Displacement 0.000807 0.001200 YES
Predicted change in Energy=-1.750931D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -12.7235 -12.7174 -6.4219 -0.0039 0.0189 0.0620
Low frequencies --- 101.0768 101.0775 147.4583
</pre>

====Summary table====

[[File:jun_ni3_sum.PNG|350px]]

====Rotatable 3d image of optimized NI3====
<jmol><jmolApplet>
<title>Optimised NI3 molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NI3_DSPACE_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

The optimised distance is 2.184 Å

=MINI PROJECT-IONIC LIQUIDS=
===[N(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_NCH3_4_FREQ.LOG|JUN_NCH3_4_FREQ.LOG]] 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000083 0.000450 YES
RMS Force 0.000044 0.000300 YES
Maximum Displacement 0.000929 0.001800 YES
RMS Displacement 0.000356 0.001200 YES
Predicted change in Energy=-3.710295D-07
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- -0.0011 -0.0007 -0.0006 34.3580 34.3580 34.3580
Low frequencies --- 216.2193 315.7261 315.7261
</pre>

====Summary table====
[[File:minip_sum1.PNG|350px]]

====Rotatable 3d image of optimized [N(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [N(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_NCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===[P(Me)4]+===
====Calculations and Optimisation====
Complete optimisation calculations and generated data can be found here [[media:JUN_PCH3_4_FREQ.LOG|JUN_PCH3_4_FREQ.LOG]]
 
B3LYP/6-31G(d,p)

<pre>
Item Value Threshold Converged?
Maximum Force 0.000035 0.000450 YES
RMS Force 0.000010 0.000300 YES
Maximum Displacement 0.000241 0.001800 YES
RMS Displacement 0.000133 0.001200 YES
Predicted change in Energy=-2.345692D-08
Optimization completed.
-- Stationary point found.
</pre>

====Low frequency lines====
<pre>
Low frequencies --- 0.0018 0.0026 0.0029 50.6302 50.6302 50.6302
Low frequencies --- 187.9222 213.0070 213.0070
</pre>

====Summary table====
[[File:minip_sum2.PNG]]

====Rotatable 3d image of optimized [P(CH3)4]+====
<jmol><jmolApplet>
<title>Optimised [P(Me)4]+ molecule</title>
<color>black</color>
<size>400</size>
<script>frame 1.16</script>
<uploadedFileContents>JUN_PCH3_4_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>