File:P FREQ ISM.LOG

2018-05-16T16:37:44Z

Iem15:

File:P opt ISM table.png

2018-05-16T16:34:13Z

Iem15:

Rep:Mod:01106385

2018-05-16T16:31:55Z

Iem15:

==BH3==

RB3LYP/6-31G(d,p)

[[File:ISM BH3 opt table2.png]]

<pre> Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000007 0.000300 YES
Maximum Displacement 0.000042 0.001800 YES
RMS Displacement 0.000027 0.001200 YES</pre>

Frequency file: [[Media:ISM BH3 FREQ.LOG| ISM BH3 FREQ.LOG]]

<pre>Low frequencies --- -7.5936 -1.5614 -0.0055 0.6514 6.9319 7.1055
Low frequencies --- 1162.9677 1213.1634 1213.1661</pre>

<jmol><jmolApplet>
<title>Optimised BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISM BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===Vibrational analysis===

{| class="wikitable"
|+
|-
|wavenumber (cm-1 || Intensity (arbitrary units) || symmetry || IR active? || type
|-
|1163
|93
|A2
|yes
|out-of-plane bend
|-
|1213
|14
|E
|yes
|bend
|-
|1213
|14
|E
|yes
|bend
|-
|2582
|0
|A1
|no
|symmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|-
|2716
|126
|E
|yes
|asymmetric stretch
|}

[[File:ISM bh3 opt spectrum.png]]

There are 6 vibrations in this molecule as shown in the table but there are only 3 peaks as shown in the spectrum. This is because there are 2 sets of degenerate vibrations: 1213 and 2716 cm-1. These degenerate vibrations each give rise to a single peak in the spectrum and one of the vibrations is not IR active so there is no peak in the spectrum corresponding to this vibration. Therefore, there is only 3 peaks in the spectrum.

===Molecular orbitals analysis===

[[File:ISM bh3 MO.png|thumb|centre|400px|Figure 1: Molecular orbital diagram for BH3<ref name="BH3_MO"/>]]

There are no significant differences between the real and LCAO molecualr orbitals (MOs) as can be seen in figure 1. This tells us that qualitative MO theory is quite accurate and useful to predict the shape of the real MOs of a molecule.

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

====NH3====

RB3LYP/6-31G(d,p)

[[File:ISM nh3 opt table.png]]

<pre> Item Value Threshold Converged?
Maximum Force 0.000006 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000008 0.001200 YES</pre>

Frequency file: [[Media:ISM NH3 FREQ.LOG| ISM NH3 FREQ.LOG]]

<pre> Low frequencies --- -8.5646 -8.5588 -0.0041 0.0455 0.1784 26.4183
Low frequencies --- 1089.7603 1694.1865 1694.1865</pre>

<jmol><jmolApplet>
<title>Optimised NH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISM NH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====NH3BH3====

RB3LYP/6-31G(d,p)

[[File:ISM nh3bh3 opt table.png]]

<pre> Item Value Threshold Converged?
Maximum Force 0.000164 0.000450 YES
RMS Force 0.000035 0.000300 YES
Maximum Displacement 0.000903 0.001800 YES
RMS Displacement 0.000344 0.001200 YES</pre>

Frequency file: [[Media:ISM NH3BH3 FREQ.LOG| ISM NH3BH3 FREQ.LOG]]

<pre>Low frequencies --- -27.8630 -0.2737 -0.0651 0.0891 11.5835 11.6805
Low frequencies --- 261.3510 631.2489 637.5432</pre>

<jmol><jmolApplet>
<title>Optimised NH3BH3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISM NH3BH3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Bond energy determination====

* E(NH3)= -56.55777 a.u.
* E(BH3)= -26.61532 a.u.
* E(NH3BH3)= -83.22469 a.u.

Using the equation ΔE=E(NH3BH3)-[E(NH3)+E(BH3)], where ΔE is the association energy, and the above reported energies, the association energy of the B-N bond is (-83.22469)-[(-56.55777)+(-26.61532)] = -0.0516 a.u. = -135.47581 kJ/mol

This is a weak bond as the bond energy is similar to the bond energy of an O-O bond (146 kJ/mol) which is a weak bond and is a lot less than the bond energy of a strong bond such as H-F (565 kJ/mol).<ref name="BE"/>

==Using Pseudo-potentials and different basis sets==

===BBr3===

RB3LYP/LanL2DZ

[[File:ISM bbr3 opt table.png]]

<pre> Item Value Threshold Converged?
Maximum Force 0.000008 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000036 0.001800 YES
RMS Displacement 0.000023 0.001200 YES</pre>

Frequency file: [[Media:ISM bbr3 freq output.log| ISM bbr3 freq output.log]]

Frequency file on DSpace: {{DOI|10042/202410}}

<pre>Low frequencies --- -0.0137 -0.0064 -0.0046 2.4315 2.4315 4.8421
Low frequencies --- 155.9631 155.9651 267.7052</pre>

<jmol><jmolApplet>
<title>Optimised BBr3 molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>ISM bbr3 freq output.log</uploadedFileContents>
</jmolApplet></jmol>

==Ionic Liquids project: Designer Solvents==

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

RB3LYP/6-31G(d,p)

[[File:N opt ISM table.png]]

<pre> Item Value Threshold Converged?
Maximum Force 0.000013 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.000767 0.001800 YES
RMS Displacement 0.000249 0.001200 YES</pre>

Frequency file: [[Media:N FREQ ISM.LOG| N FREQ ISM.LOG]]

<pre>Low frequencies --- -22.2614 -14.9273 -11.4472 -0.0010 -0.0007 0.0002
Low frequencies --- 180.5332 281.8698 286.4332</pre>

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

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

RB3LYP/6-31G(d,p)

[[File:IEM pch34 opt table.png]]

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

Frequency file: [[Media:IM PCH34 FREQ.LOG| IM PCH34 FREQ.LOG]]

<pre>Low frequencies --- -0.0027 -0.0023 0.0020 51.2698 51.2698 51.2699
Low frequencies --- 186.5950 211.3905 211.3905</pre>

<jmol><jmolApplet>
<title>Optimised [P(CH3)4]+ molecule</title>
<color>black</color>
<size>200</size>
<uploadedFileContents>IM PCH34 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NBO charge analysis===

[[File:IEM nch34 charge.png|thumb|Figure 2: Charge distribution of [N(CH3)4]+]]

[[File:IEM pch34 charge.png|thumb|Figure 3: Charge distribution of [P(CH3)4]+]]

As can be seen in figures 2 and 3 the charge distribution in the two cations vary quite a lot:

* [N(CH3)4]+:
** Central nitrogen atom: -0.295
** Carbon atoms: -0.483
** Hydrogen atoms: 0.269

* [P(CH3)4]+:
** Central phosphorus atom: 1.666
** Carbon atoms: -1.060
** Hydrogen atoms: 0.298

The main difference here is that the central atom in the nitrogen compound has a negative charge whereas the central atom in the phosphorus compound has a positive charge. This is because C has a higher electronegativity value (2.55) than phosphorus (2.19) but lower than the value for nitrogen (3.04). This leads to the N-C bond being polar with the N atom having the electron density on it so it has a negative charge. This is opposite to the P-C bond where the electron density is on the C atom and therefore, the P atom has a positive charge. This is also the basis of the reason that the C atoms have a more negative charge in the P compound than they do in the N compound as the C atom gets the electron density from the C-H bond (H electronegativity: 2.20) in both compounds, therefore, this electron density combines with the electron density from the P-N bond and the charge is more negative than it is in the N compound where this doesn't happen and is only negative due to the delta negative charge from the C-H bond.<ref name="EN"/>

[[File:NR4 charge example.png|thumb|Figure 4: [NR4]+ (R=alkyl) as often depicted<ref name="NR4"/>]]

As can been in figure 4, a positive charge is often placed on the N atom in a depiction of [NR4]+, this charge represents the charge of the overall compound being +1, but as can be seen above, the actual charge on the N atom isn't positive, rather it is negative. The positive charge is actually located on hydrogen atoms as shown in figure 2.

===MO analysis===

<references>
<ref name="BH3_MO">Hunt, P. (n.d.). ''Lecture 4 Tutorial - MO diagram for BH3.'' [ebook] p.3. Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf.</ref>
<ref name="BE">Petrucci, R., Herring, F., Madura, J. and Bissonnette, C. (n.d.). ''General chemistry'', '''2015'''.</ref>
<ref name="EN">Helmenstine, T. (2018). ''List of Electronegativity Values of the Elements.'' [online] Science Notes and Projects. Available at: https://sciencenotes.org/list-of-electronegativity-values-of-the-elements/ [Accessed 16 May 2018].</ref>
<ref name="NR4">Hunt, P. (n.d.). Computational Inorganic Chemistry: Hunt Research Goup, Imperial College London. [online] Huntresearchgroup.org.uk. Available at: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/12c_ionic_liquids.html [Accessed 16 May 2018].</ref>
</references>

File:N FREQ ISM.LOG

2018-05-16T16:30:34Z

Iem15:

File:ISM BH3 opt table2.png

2018-05-15T15:43:28Z

Iem15:

File:ISM bh3 opt table.png

2018-05-15T15:41:03Z

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