View source for Inorganic lab sb1016

= Computational Analysis of Molecules and their properties =

== BH<sub>3</sub>  ==
BH<sub>3</sub> molecule was analysed using '''B3LYP/6-31G(d,p) '''method/basis set and the following parameters were obtained.
{| class="wikitable"
|-
|Optimized Bond Length
|119.99
|-
|Optimized Bond Angle
|120.0
|}

<jmol><jmolApplet>
  <title>Optimised Borane Molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>sb1016_bh3_opt.log</uploadedFileContents>
</jmolApplet></jmol>

The optimisation log file is linked [[Media:sb1016_bh3_opt.log|here]]

From the optimisation, the summary of the results are presented below:

[[File:sb1016_bh3_summary.JPG]]

From the table presented below, it can also be seen that the optimisation was successful as the results have converged.

<pre>Item               Value     Threshold  Converged?
 Maximum Force            0.000006     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000025     0.001800     YES
 RMS     Displacement     0.000016     0.001200     YES</pre>

=== Frequency Analysis for BH<sub>3</sub>: ===
The "zero" frequencies are within the required limits of -15 to +15. 

<pre>Low frequencies ---   -0.9602   -0.9310   -0.0054    5.3142   11.5142   11.5542
Low frequencies --- 1162.9948 1213.1816 1213.1843</pre>

Frequency Log file of BH<sub>3</sub> can be found [[Media:sb1016_bh3_freq.log|here]]

Vibrational Spectrum for BH<sub>3</sub>

{| class="wikitable"
!Wavelength(cm<sup>-1</sup>)
!Intensity(arbitrary units)
!Symmetry
!IR peak
!Type
|-
|1162
|317
|A1
|Active
|Out of plane bend
|-
|1213
|46
|E
|Active (Low intensity)
|Asymmetric bend
|-
|1213
|46
|E
|Active (Low intensity)
|Bend
|-
|2582
|0
|A1
|Not-Active
|Symmetric Stretch
|-
|2715
|185
|E
|Active (Low intensity)
|Asymmetric stretch
|-
|2715
|185
|E
|Active (Low intensity)
|Asymmetric stretch
|}

IR analysis of BH<sub>3</sub>

[[File:sb1016_bh3_ir.jpg|IR spectrum of BH<sub>3</sub>.]]

Even though there are 6 frequencies, only three are observed. The vibration at 2582 cm<sup>-1</sup> is symmetric and therefore, is not observed in the IR spectrum. There are two pairs of vibrations at 1213 cm<sup>-1</sup> and 2715 cm<sup>-1</sup>. The vibrations at each of these frequencies have the same intensity as well. As they are degenerate, they overlap and only one peak is observed for each pair. Due to these reasons, only 3 peaks are observed.

[[User:Smf115|Smf115]] ([[User talk:Smf115|talk]]) 16:06, 28 May 2018 (BST)Good explanation of why only three peaks are visible mentioning both the degeneracy and IR inactivity of some of the peaks. However, although your frequency log file shows the molecule to be the correct point group (D3h) your symmetry assignments are incorrect and the IR intensities are also wrong. Both of these values can be read from your frequency log file after the low frequencies section.

=== Molecular Orbital Analysis of BH<sub>3</sub> ===
A qualitative MO diagram for BH<sub>3</sub> is presented below.

[[File:sb1016_bh3_mo_full.jpg|center|400px|MO diagram of BH<sub>3</sub>.]]

{| class="wikitable"
!Real MOs
!LCAOs from MO diagram
!Comments
|-
|[[File:sb1016_bh3_mo1.jpg|200px]]
|
|This is the non-bonding s-orbital of B (deep in energy)
|-
|[[File:sb1016_bh3_mo2.jpg|200px]]
|[[File:sb1016_bh3_1.jpg|200px]]
|Lowest energy valence a<sub>1</sub><sup>'</sup> MO. Both the LCAO and the real MO

seem very similar in shape
|-
|[[File:sb_bh3_mo4.jpg|200px]]
|[[File:sb1016_bh3_2.jpg|200px]]
|Both the real MO and LCAO are very similar.
|-
|[[File:sb1016_bh3_mo3.jpg|200px]]
|[[File:sb1016_bh3_3.jpg|200px]]
|High similarity between the real MO and the representation 
|-
|[[File:sb_bh3_mo5.jpg|200px]]
|[[File:sb_bh3_4.jpg|200px]]
|Unoccupied Orbital:

It can be seen that the orbital is positioned in the 

z-direction (out of the plane of the molecule) in both the real MO

and the representation. 

|-
|[[File:sb_bh3_mo6.jpg|200px]]
|[[File:sb_bh3_5.jpg|200px]]
|Unoccupied Orbital:

The orbital representations are very similar. However, the MOs

in from the calculations seem to be more diffuse.
|-
|[[File:sb_bh3_mo7.jpg|200px]]
|
|Unoccupied Orbital
|-
|[[File:sb_bh3_mo8.jpg|200px]]
|
|Unoccupied Orbital
|}
The high degree of similarity between the LCAOs and the real MOs suggest that the technique used for the optimization of BH<sub>3</sub> molecule and its frequency analysis is accurate. It also marks the importance and accuracy of MO theory in predicting properties and structure of molecules. This also shows that MO theory can be used to predict the molecular orbitals of more complex systems as well.

== Ammonia ==

NH<sub>3</sub> molecule was analysed using '''B3LYP/6-31G(d,p) '''method/basis set.

<jmol><jmolApplet>
  <title>Optimised Ammonia molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>sb1016_nh3_opt.LOG</uploadedFileContents>
</jmolApplet></jmol>

A summary of the results obtained is presented below:

[[File:sb1016_nh3_summary.JPG]]

The optimisation log file can be found [[Media:sb1016_nh3_opt.LOG|here]]

<pre>Item               Value     Threshold  Converged?
 Maximum Force            0.000006     0.000450     YES
 RMS     Force            0.000004     0.000300     YES
 Maximum Displacement     0.000016     0.001800     YES
 RMS     Displacement     0.000011     0.001200     YES</pre>

The optimisation was successful as the parameters have converged. 

Frequency analysis of NH<sub>3</sub>

Frequency log file can be found [[Media:sb1016_nh3_freq.LOG|here]]

<pre> Low frequencies ---   -8.5223   -8.4750   -0.0029    0.0335    0.1918   26.4067
 Low frequencies --- 1089.7616 1694.1862 1694.1866</pre>

The "zero" frequencies are a little above the allowed range. However, these frequencies are much lower than the first vibrational frequency of 1089 cm<sup>-1</sup>. Moreover, these high "zero" frequencies are due to the low computational level and basis set and can be corrected by performing the calculation with a better method.

== Ammonia Borane ==

Ammonia Borane calculation were carried out with '''B3LYP/6-31G(d,p). '''

<jmol><jmolApplet>
  <title>Optimised Molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>sb_nb_opt.LOG</uploadedFileContents>
</jmolApplet></jmol>

A summary of the optimisation is presented below:

[[File:sb1016_nb_summary.JPG]]

The optimisation log file can be found [[Media:sb_nb_opt.LOG|here]]

<pre>Item               Value     Threshold  Converged?
 Maximum Force            0.000037     0.000450     YES
 RMS     Force            0.000019     0.000300     YES
 Maximum Displacement     0.000379     0.001800     YES
 RMS     Displacement     0.000173     0.001200     YES</pre>

It can be seen that the parameters have converged and that the optimisation is successful. 

The frequency log file from the frequency analysis can also be found [[Media:sb1016_nb_freq.LOG|here]]

<pre>Low frequencies ---   -8.4231   -0.0746   -0.0066    0.2378   13.2406   13.2506
Low frequencies ---  262.9935  632.8261  639.1009</pre>

The "zero" frequencies are below the specified range. 

=== Energy Analysis of N-B dative bond ===
The association energy of Ammonia and Borane was calculated using ΔE = E(NH<sub>3</sub>BH<sub>3</sub>)-[E(NH<sub>3</sub>)+E(BH<sub>3</sub>)]. 
{| class="wikitable"
!
!Energy
|-
|NH<sub>3</sub>
|<nowiki>-56.557 a.u.</nowiki>
|-
|BH<sub>3</sub>
|<nowiki>-26.615 a.u.</nowiki>
|-
|NH<sub>3</sub>BH<sub>3</sub>
|<nowiki>-83.224 a.u.</nowiki>
|-
|Association
|<nowiki>-0.0515 a.u.</nowiki>
|-
|Association
|<nowiki>-135 ± 10 kJ/mol</nowiki>
|}
The N-B dative bond has medium strength as it is around one-third the strength of a normal N-B covalent bond and N-H covalent bond (~300kJ/mol).

== BBr<sub>3</sub> ==

BBr<sub>3</sub> was analysed using B3LYP/Gen method/basic set. The PPs used for Br atoms was LanL2DZ potential, whereas for B 6-31G(d,p) was used. 

<jmol><jmolApplet>
  <title>Optimised Molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>sb1016_bbr3_opt.log</uploadedFileContents>
</jmolApplet></jmol>

[[file:sb1016_bbr3_summary.JPG]]

From the table presented below, it can be seen that all the parameters have converged and that the optimization was a success. 

<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>

The optimization log file is linked [[Media:sb1016_bbr3_opt.log|here]]

the frequency log file is linked [[Media:sb1016_bbr3_freq.log|Click here]]

<pre>Low frequencies ---   -0.0137   -0.0064   -0.0046    2.4315    2.4315    4.8421
 Low frequencies ---  155.9631  155.9651  267.7052</pre>
The "zero" frequencies are within the specifies range and are lower than the first vibrational frequency.

[[User:Smf115|Smf115]] ([[User talk:Smf115|talk]]) 16:13, 28 May 2018 (BST)Well presented structure informaition throughout and nice reporting of the computational method and basis set used, including the pseudopotential here.

== Investigation of Ionic Liquids ==

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

N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> was analysed using '''B3LYP/6-31G(d,p) ''' method/baiss set. 

<jmol><jmolApplet>
  <title>Optimised Molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>sb1016_nr_opt.LOG</uploadedFileContents>
</jmolApplet></jmol>

The summary of the optimization is presented below:

[[File:Summary.JPG]]

The optimization log file can be found [[Media:sb1016_nr_opt.LOG|here]]

<pre>Item               Value     Threshold  Converged?
 Maximum Force            0.000067     0.000450     YES
 RMS     Force            0.000017     0.000300     YES
 Maximum Displacement     0.000146     0.001800     YES
 RMS     Displacement     0.000081     0.001200     YES</pre>

As all the parameters have converged, it can be concluded that the optimization was a success. 

<pre>Low frequencies ---   -0.0005    0.0001    0.0007   35.2977   35.2977   35.2977
 Low frequencies ---  217.4078  316.4871  316.4871</pre>

However, the "zero" frequencies are above the allowed range of ±15 cm-1. This might be a result of low level basis set, relaxed convergence and poor integration criteria. Further calculations can be carried out with a better basis set. 

The frequency log file can be found [[Media:sb1016_nr_freq.LOG|here]]

===== Valence Molecular Orbitals =====
In N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>, the MOs follow the symmetry of the point group which is Td. Therefore, for the nitrogen, there are triply degenerate "p" orbitals.  This nature of the orbitals gives rise to highly symmetric MOs. However, for the representation below, these degenerate orbitals are just represented as normal p-orbitals on the nitrogen. 

[[File:sb_nitrogen.JPG|thumb|Nitrogen's Triply degenerate p-orbitals]]

{| class="wikitable"
!Real MOs
!Fragment Orbitals
!Simplified MOs
!Comment
|-
|[[File:sb_nr_real_mo6.jpg|200px]]
|[[File:sb_nr_6_frag.JPG]]
|[[File:sb_nr_6_lcao.JPG]]
|This MO is a bonding orbital with the lowest energy. The electron density seems to be diffused throughout the whole structure. 
|-
|[[File:sb_nr_real_mo15.jpg|200px]]
|[[File:sb_nr_frag_15.JPG]]
|[[File:sb_nr_15_lcao.JPG]]
|This MO is a non-bonding orbital from the methyl part of the molecule. 
|-
|[[File:sb_nr_real_mo19.jpg|200px]]
|[[File:sb_nr_frag_19.JPG]]
|[[File:sb1016new19lcao.JPG]]
|This MO is high in energy and is an anti-bonding orbital.
|}

[[User:Smf115|Smf115]] ([[User talk:Smf115|talk]]) 19:16, 1 June 2018 (BST)The FOs and LCAOs are clearly depicted and are correct for the MOs visualised, however, which MOs these are has not been labelled.

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

Even though phosphorous is in third period, it is not big enough to use the "Gen" method. Therefore, the calculations were carried out using the '''B3LYP/6-31G(d,p) ''' method/basis set. 

<jmol><jmolApplet>
  <title>Optimised Molecule</title>
  <color>black</color>
  <size>200</size>
  <uploadedFileContents>sb1016_pr_opt.LOG</uploadedFileContents>
</jmolApplet></jmol>

Summary of optimization:

[[File:sb1016_pr_summary.JPG]]

As all the parameters have converged, it can be concluded that the optimization was a success.

<pre>Item               Value     Threshold  Converged?
 Maximum Force            0.000136     0.000450     YES
 RMS     Force            0.000036     0.000300     YES
 Maximum Displacement     0.000498     0.001800     YES
 RMS     Displacement     0.000348     0.001200     YES</pre>

The optimization log file is linked [[Media:sb1016_pr_opt.LOG|here]]

<pre>Low frequencies ---   -0.0023   -0.0017    0.0012   51.3471   51.3471   51.3471
 Low frequencies ---  186.8184  211.5721  211.5721</pre>

The "zero" frequency is once again, above the allowed range, as a result of the low level of the basis set used. However, it is smaller than the first vibrational frequency and this margin is adequate for this calculation. This margin can be reduced by using a better method and basis set.  

Frequency Log file is linked [[Media:sb1016_pr_freq.LOG|here]]

The MOs for this cation will be similar to the N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup> cation. However, the orbitals will be more diffuse. Further analysis can be carried out on these orbitals to compute the key differences in electron density distribution and reactivity.

=== NBO Charge Analysis ===
For both the structures analysed above, according to the lewis structures, the formal charge is +1. This shows that in this structure, the central atom (N/P) donates an electron to one of the methyl groups and gains a formal +1 charge. 
{| class="wikitable"
!Molecule
!NBO Charges
!Charge on the central atom
!Charge on Carbon Atoms
!Comment
|-
|P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>
|[[File:sb_pr_nbo.JPG|200px]]
|<nowiki>+1.660</nowiki>
|<nowiki>-1.060</nowiki>
|For the P(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>,  the phosphorous atom has a charge higher than +1. As phosphorous is a relatively large molecule, this cation's electron density is very diffuse. Therefore, a large part of the electron density lies at the carbon, making at delta negative. 
|-
|N(CH<sub>3</sub>)<sub>4</sub><sup>+</sup>
|[[File:sb_nr_nbo.JPG|200px]]
|<nowiki>-0.295</nowiki>
|<nowiki>-0.483</nowiki>
|In the N(CH<sub>3</sub>)<sub>4</sub><sup>+ </sup> cation, both the nitrogen and the carbon atoms have a partial negative charge. However, the nitrogen atom is less delta negative than the carbon. There is no positive charge on the nitrogen. This might be due to the close electronegativites of N and C. Nitrogen is also a smaller atom compared to phosphorous, preventing the electron density from diffusing more. This also shows that the phoshorous cation is more susceptible to nucleophilic attack than the nitrogen cation. 
|}

[[User:Smf115|Smf115]] ([[User talk:Smf115|talk]]) 15:46, 1 June 2018 (BST)Good consideration and comparison of the charges on the main metal cation. However, the same colour range should have been used to highlight the charge distribution across the molecules and the charges on the Me groups and bond polarities should have also been discussed.