View source for Zcj17y2comp

===EX<sub>3</sub> Section===

====BH<sub>3</sub>====

'''B3LYP/6-61G level'''

[[Image:Zcj17BH3 2 sym opt631g dp.PNG|thumb|center|BH<sub>3</sub> Summary Table]]

'''Item Table'''
<pre>
Item               Value     Threshold  Converged?
 Maximum Force            0.000009     0.000450     YES
 RMS     Force            0.000006     0.000300     YES
 Maximum Displacement     0.000019     0.001800     YES
 RMS     Displacement     0.000011     0.001200     YES
</pre>


Frequency analysis log file:[[BH<sub>3</sub>|https://wiki.ch.ic.ac.uk/wiki/images/c/c2/ZCJ17_BH3_FREQ.LOG]]

'''Low Frequency Table'''
<pre>
Low frequencies ---   -7.5936   -1.5614   -0.0054    0.6514    6.9319    7.1055
 Low frequencies --- 1162.9677 1213.1634 1213.1661
</pre>

{| class="wikitable"
|-
! Wavenumber (cm<sup>-1<sup>)
! Intensity (arbitrary)
! Symmetry
! IR Active?
! Type
|-
| 1163
| 92.6
| A''<sub>2</sub>
| Yes
| Out-of-plane bend
|-
| 1213
| 14.0
| E'
| Very slight
| In-plane bend
|-
| 1213
| 14.0
| E'
| Very slight
| In-plane bend
|-
| 2582
| 0
| A'<sub>1</sub>
| No
| Totally symmetric stretch
|-
| 2716
| 126.3
| E'
| Yes
| Asymmetric stretch
|-
| 2716
| 126.3
| E'
| Yes
| Asymmetric stretch
|}

'''IR Spectrum'''
[[image:ZCJIR Spectrum.PNG|center|BH<sub>3</sub> IR Spectrum]]

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 23:46, 21 May 2019 (BST) Why are there only three peaks in your IR spectrum?

'''JMol'''
<jmol><jmolApplet>
  <title> optimised BH<sub>3</sub> molecule</title>
  <color>lightgrey</color>
  <size>200</size>
  <uploadedFileContents>ZCJ17_BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===BH<sub>3</sub> MO Diagram===

[[image:ZCJ17Completed annotated MO diagram.PNG|centre|BH<sub>3</sub> MO Diagram]]

Diagram adapted from http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

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

There are some significant differences between the MOs formed from the LCAO process and the computer-generated MOS. Firstly, The The LCAO MOs are simply superimposed atomic orbitals. This means it is not possible to see the total effect on placing two orbitals near each other. In contrast the 'real' MOS are created by fully calculating the effect of all of the different atomic or fragment orbitals involved. This means they appear more diffuse and, in some cases, less clear in precisely which orbitals are involved. 

====What does this say about the accuracy and usefulness of qualitative MO theory?====
 
The LCAO MOs are more qualitative and therefore, are less accurate as a true picture of molecular orbitals as the computer generated MOs. This inherently makes them less useful in complex molecular analysis. However, they do have some use in identifying specifically which atomic orbitals are involved in certain bonding interactions.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 23:52, 21 May 2019 (BST) Whilst MO theory doesn't predict the exact shape of the MOs, this isn't the most major difference. What about the relative contributions of the individual AOs?

===NH<sub>3</sub>BH<sub>3</sub>===

====NH<sub>3</sub>====
'''B3LYP/6-61G level'''

[[image:ZCJNH3 3 sym opt631g dp.PNG|thumb|centre|NH<sub>3</sub> Symmetry Table]]

'''Item Table'''
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000009     0.000450     YES
 RMS     Force            0.000006     0.000300     YES
 Maximum Displacement     0.000019     0.001800     YES
 RMS     Displacement     0.000011     0.001200     YES
</pre>


Frequency analysis log file:[[NH<sub>3</sub>|https://wiki.ch.ic.ac.uk/wiki/images/2/21/ZCJ_NH3_3_FREQ.LOG]]

'''Low Frequency Table'''
<pre>
Low frequencies ---   -8.5223   -8.4750   -0.0037    0.0334    0.1918   26.4067
 Low frequencies --- 1089.7616 1694.1862 1694.1866
</pre>

'''JMol'''
<jmol><jmolApplet>
  <title>optimised NH<sub>3</sub> molecule</title>
  <color>lightgrey</color>
  <size>200</size>
  <uploadedFileContents>ZCJ NH3 3 FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

===NH<sub>3</sub>BH<sub>3</sub>===

'''B3LYP/6-61G level'''


[[image:ZCJNH3BH table.PNG|thumb|centre|NH<sub>3</sub>BH<sub>3</sub> Summary Table]]

'''Item Table'''
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000139     0.000450     YES
 RMS     Force            0.000063     0.000300     YES
 Maximum Displacement     0.000771     0.001800     YES
 RMS     Displacement     0.000338     0.001200     YES
</pre>


Frequency analysis log file:[[NH<sub>3</sub>BH<sub>3</sub>|https://wiki.ch.ic.ac.uk/wiki/images/7/72/ZCJNH3BH3_FREQ.LOG]]

'''Low Frequency Table'''
<pre>
 Low frequencies ---   -0.0614   -0.0448   -0.0066   22.0873   22.0930   40.5268
 Low frequencies ---  265.8900  632.3722  640.1154
</pre>

'''JMol'''
<jmol><jmolApplet>
  <title>optimised BH<sub>3</sub> molecule</title>
  <color>lightgrey</color>
  <size>200</size>
  <uploadedFileContents>ZCJNH3BH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Energies====

E(NH<sub>3</sub>)= -56.5578 a.u.

E(BH<sub>3</sub>)= -26.61532 a.u. 

E(NH<sub>3</sub>BH<sub>3</sub>)= -83.2247 a.u.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 23:58, 21 May 2019 (BST) You've rounded to early here. Your results should be reported to 5 d.p. and then your final answer is rounded to the nearest kJ/mol. Because you rounded to early, your answer is off by 1 kJ/mol.

ΔE=E(NH<sub>3</sub>BH<sub>3</sub>)-[E(NH<sub>3</sub>)+E(BH<sub>3</sub>)

  =-83.22469 - [-56.55777 + -26.6153]
  = -0.05162 a.u.
  = -136 kJ/mol

The N-B bond energy is fairly weak. In comparison, a C-C single bond in ethene is 347 kJ/mol (from http://butane.chem.uiuc.edu/cyerkes/Chem104ACSpring2009/Genchemref/bondenergies.html|date accessed 10/05/19), which is about 2.5 times the strength.

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 23:58, 21 May 2019 (BST) A book source would be better here.

===NI<sub>3</sub>===

'''B3LYP/6-61G level'''


[[image:ZCJ NI3 opt.PNG|thumb|centre|NI<sub>3</sub> Summary Table]]

'''Item Table'''
<pre>
Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000450     YES
 RMS     Force            0.000002     0.000300     YES
 Maximum Displacement     0.000022     0.001800     YES
 RMS     Displacement     0.000014     0.001200     YES
</pre>


Frequency analysis log file:[[NI<sub>3</sub>|https://wiki.ch.ic.ac.uk/wiki/images/e/e6/ZCJ_NI3_FREQ.LOG]]

'''Low Frequency Table'''
<pre>
 Low frequencies ---  -12.5522  -12.5460   -6.0047   -0.0040    0.0191    0.0664
 Low frequencies ---  100.9969  100.9977  147.3377
</pre>

'''JMol'''
<jmol><jmolApplet>
  <title>optimised BH<sub>3</sub> molecule</title>
  <color>lightgrey</color>
  <size>200</size>
  <uploadedFileContents>ZCJ_NI3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

N-I optimised distance- 2.1840 Å

===Project Section===



====N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>====


'''B3LYP/6-61G level'''


[[image:ZCJ NCH3 opt.PNG|thumb|centre|N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> Summary Table]]

'''Item Table'''
<pre>
         Item               Value     Threshold  Converged?
 Maximum Force            0.000073     0.000450     YES
 RMS     Force            0.000018     0.000300     YES
 Maximum Displacement     0.000277     0.001800     YES
 RMS     Displacement     0.000088     0.001200     YES
</pre>


Frequency analysis log file:[[File:N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>|https://wiki.ch.ic.ac.uk/wiki/images/7/79/ZCJ_NCH3_FREQ.LOG]]

'''Low Frequency Table'''
<pre>
Low frequencies ---   -0.0008   -0.0006   -0.0002   35.6259   35.6259   35.6259
 Low frequencies ---  215.5175  315.1186  315.1186
</pre>

'''JMol'''
<jmol><jmolApplet>
  <title>optimised N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> molecule</title>
  <color>lightgrey</color>
  <size>200</size>
  <uploadedFileContents>ZCJ_NCH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>====


'''B3LYP/6-61G level'''

[[image:ZCJ PCH3 opt.PNG|thumb|centre|P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> Summary Table]]

'''Item Table'''
<pre>
Item               Value     Threshold  Converged?
 Maximum Force            0.000138     0.000450     YES
 RMS     Force            0.000035     0.000300     YES
 Maximum Displacement     0.000718     0.001800     YES
 RMS     Displacement     0.000298     0.001200     YES
</pre>


Frequency analysis log file:[[P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>|https://wiki.ch.ic.ac.uk/wiki/images/d/d5/ZCJ_PCH3_FREQ.LOG]]

'''Low Frequency Table'''
<pre>
Low frequencies ---   -0.0024   -0.0023   -0.0016   51.6355   51.6355   51.6355
 Low frequencies ---  188.7455  213.5999  213.5999
</pre>

'''JMol'''
<jmol><jmolApplet>
  <title>optimised P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> molecule</title>
  <color>lightgrey</color>
  <size>200</size>
  <uploadedFileContents>ZCJ_PCH3_FREQ.LOG</uploadedFileContents>
</jmolApplet></jmol>

====Charges====

[[Image:ZCJPCH3 charge.PNG|thumb|center|P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>]]
[[Image:ZCJNCH3 charge.PNG|thumb|center|N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>]]

{| class="wikitable"
|-
! Atom
! Electronegativity (from http://www.rsc.org/periodic-table/trends)
|-
| Phosphorous 
| 2.19
|-
| Nitrogen
| 3.04
|-
| Carbon
| 2.55
|}


{| class="wikitable"
|-
! Atom
! P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>
! N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>
! Notes
|-
| P/N 
| 1.666
| -0.295
| rowspan=3|The phosphorous charge is positive, whereas the nitrogen's is negative. This is due to the difference in electronegativities. Nitrogen has an electronegativity of 3.04, whereas phosphorous has an electronegativity of 2.19. A low electronegativity means an atom can more easily stabilise a positive charge. In the nitrogen cation, the positive charge is shared between the nitrogen and the carbons. In the phosphorous cation, the charge is more localised to the phosophorous atom, however in all cases, charge is spread around the molecule to a certain extent
|-
| Carbon
| -1.060
| -0.483
|-
| Hydrogen
| 0.298
| 0.269
|}

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 00:04, 22 May 2019 (BST) You should also discuss the charges on other atoms, as well as provide a discussion about differences between the formal charge picture and the calculated NBOs.

====MOs====

[[User:Ng611|Ng611]] ([[User talk:Ng611|talk]]) 00:09, 22 May 2019 (BST) Good LCAO analysis! I'd label your interactions on the LCAO diagram instead of describing them in a paragraph under the diagrams. 

[[Image:ZcjMYLCAOMO6.PNG|thumb|left|LCAO for MO6]]
[[Image:ZcjMYMO6.PNG|thumb|center|Real MO6]]
 
This MO is totally bonding. It is constructed from the 1s hydrogen orbitals and the 2s carbon and nitrogen oribitals all constructively overlapping


[[Image:ZcjMYLCAOMO8.PNG|thumb|left|LCAO for MO8]]
[[Image:ZCJMYMO8.PNG|thumb|center|Real MO]]

This MO is also totally bonding. It is constructed from  the 1s hydrogen orgitals overlapping constructively with a carbon 2s orbital. These ligands then overlap constructively witht he nitrogen 2p orbitals, 2 as is, and 2 with inverted phase. 

[[Image:ZCJLAST MO.PNG|thumb|left|LCAO for MO20]]
[[Image:ZCJ17MYMO20.PNG|thumb|center|Real MO]]

This is also a bonding orbital, with some antibonding charactetr through space. It is constructed from the hydrogen 1s orbitals overlapping in phase witht the carbon 2p orbital which is is then overlapping in phase again with the nitrogen 2p orbital for each ligand.