Difference between revisions of "Wolfeka"

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 +
==to do==
 +
*redo some of the accuracies
 +
tabulate and compare all the H---Cl distances for all ion-pairs.
 +
how do the H-bonds of Me3NH and HMim compare?
 +
how do the H-bonds of the N-H and C-H H-bonds compare?
 +
are these distances representative of a H-bond? Hint compare your distances to the sum of the van der waals radii of H and Cl.
 +
will the ionic nature of the ions effect a distance based assessment of H-bonding?
 +
provide a table and comparison of the association energy for a-c
 +
make this explicit, so give the energy of each component in atomic units, compute the deltaE in au and then convert to kJ/mol
 +
provide the relative energy of the two isomers (a) and (b), ask if you are not sure what this is.
 +
rationalise why one conformer is less stable than the other.
 +
discuss the dissociation energy of (c) relative to (a) and (b). What does the comparison tell us about the H-bonding?
 +
scan the N-H coordinate towards Cl of (a)
 +
take your optimised (a)structure, swap atoms to make N=1 and H=2, set the N-H distance to 0.8 and the N-Cl distance to 3.2, run the scan. This will take some time, start it early!
 +
provide a snapshot from gaussview of the "raw" HMim-Cl PES plot
 +
provide a chemical diagram of the two protonation states for HMim-Cl
 +
graph the MeNH-Cl and HMim-Cl scans on a single PES plot
 +
discuss your HMim-Cl PES plot, compare and contrast your results for the MeNH-Cl and HMim-Cl PES.
 +
 +
==1-methyl-imidazolium chloride==
 +
===Calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file|| KATW_RINGA_OPTFREQ2.log
 +
|-
 +
|molecule|| 1-methyl-imidazolium chloride A
 +
|-
 +
|method|| RB3LYP
 +
|-
 +
|basis set|| 3-21G
 +
|-
 +
|final energy||-722.68731au
 +
|-
 +
|RMS gradient||5.198e-06au/bohr
 +
|-
 +
|point group|| C1
 +
|}
 +
 +
 +
===Item table===
 +
Optimizing item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000011    0.000450    YES
 +
RMS    Force            0.000003    0.000300    YES
 +
Maximum Displacement    0.001137    0.001800    YES
 +
RMS    Displacement    0.000246    0.001200    YES
 +
</pre>
 +
 +
Frequency item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000011    0.000450    YES
 +
RMS    Force            0.000003    0.000300    YES
 +
Maximum Displacement    0.001332    0.001800    YES
 +
RMS    Displacement    0.000305    0.001200    YES
 +
</pre>
 +
 +
 +
====Key bond distances and angles====
 +
*add another decimal point to each
 +
{| class="wikitable"
 +
|r(H-Cl) bond distance|| 1.719&Acirc;
 +
|}
 +
 +
===File history===
 +
[[Media:KATW RINGA OPTFREQ2.LOG]]
 +
 +
 +
===1-methyl-imidazolium chloride A frequencies===
 +
<pre>
 +
Low frequencies ---  -5.2962  -2.8134  -0.0015    0.0024    0.0026    2.7809
 +
Low frequencies ---  36.1361  64.4953  80.8261
 +
</pre>
 +
The initial frequency scan resulted in a negative frequency vibration from the methyl group. The methyl group was manually rotated and the scan run again with reading internal force constants to yield better data.
 +
 +
===Calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file|| KATW RINGB OPTFREQ2.LOG
 +
|-
 +
|molecule|| 1-methyl-imidazolium chloride B
 +
|-
 +
|method|| RB3LYP
 +
|-
 +
|basis set|| 3-21G
 +
|-
 +
|final energy||-722.6662au
 +
|-
 +
|RMS gradient||2.5631e-05au/bohr
 +
|-
 +
|point group|| C1
 +
|}
 +
 +
 +
===Item table===
 +
Optimizing item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000088    0.000450    YES
 +
RMS    Force            0.000020    0.000300    YES
 +
Maximum Displacement    0.000693    0.001800    YES
 +
RMS    Displacement    0.000163    0.001200    YES
 +
</pre>
 +
 +
Frequency item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000088    0.000450    YES
 +
RMS    Force            0.000020    0.000300    YES
 +
Maximum Displacement    0.001343    0.001800    YES
 +
RMS    Displacement    0.000321    0.001200    YES
 +
</pre>
 +
 +
 +
====Key bond distances and angles====
 +
*add another decimal point to each
 +
{| class="wikitable"
 +
|r(CH-Cl) bond distance|| 2.134&Acirc;
 +
|-
 +
|r(CH2H-Cl) bond distance|| 2.277&Acirc;
 +
|}
 +
 +
===File history===
 +
[[Media:KATW RINGB OPTFREQ2.LOG]]
 +
 +
 +
===1-methyl-imidazolium chloride B frequencies===
 +
<pre>
 +
Low frequencies ---  -6.2380  -3.1641    0.0011    0.0033    0.0040    1.3698
 +
Low frequencies ---  45.3380  162.1734  198.8517
 +
</pre>
 +
 +
 +
===Calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file|| KATW_RINGC_OPTFREQ.log
 +
|-
 +
|molecule|| 1-methyl-imidazolium chloride C
 +
|-
 +
|method|| RB3LYP
 +
|-
 +
|basis set|| 3-21G
 +
|-
 +
|final energy||-761.77953au
 +
|-
 +
|RMS gradient||8.305e-06au/bohr
 +
|-
 +
|point group|| C1
 +
|}
 +
 +
 +
===Item table===
 +
Optimizing item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000027    0.000450    YES
 +
RMS    Force            0.000005    0.000300    YES
 +
Maximum Displacement    0.000555    0.001800    YES
 +
RMS    Displacement    0.000154    0.001200    YES
 +
</pre>
 +
 +
Frequency item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000027    0.000450    YES
 +
RMS    Force            0.000005    0.000300    YES
 +
Maximum Displacement    0.000581    0.001800    YES
 +
RMS    Displacement    0.000167    0.001200    YES
 +
</pre>
 +
 +
 +
====Key bond distances and angles====
 +
{| class="wikitable"
 +
|r(H-Cl) bond distance|| 2.030&Acirc;
 +
|}
 +
 +
===File history===
 +
[[Media:KATW RINGC OPTFREQ.LOG]]
 +
 +
 +
===1-methyl-imidazolium chloride C frequencies===
 +
<pre>
 +
Low frequencies ---  -3.7052  -3.0699  -0.0042  -0.0027  -0.0019    2.2969
 +
Low frequencies ---  52.1621  102.5835  107.1578
 +
</pre>
 +
 +
 +
 +
== Me<sub>3</sub>NH Cl molecule ==
 +
===Calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file|| KATW_Me3NH-Clactual.log
 +
|-
 +
|molecule||  Me<sub>3</sub>NH Cl
 +
|-
 +
|method|| RB3LYP
 +
|-
 +
|basis set|| 6-31G(d,p)
 +
|-
 +
|final energy||-635.31113au
 +
|-
 +
|RMS gradient||4.0214e-05au/bohr
 +
|-
 +
|point group|| C1
 +
|}
 +
 +
The above point group was not set to be C3v, which it should be, so the program assigned it C1.
 +
 +
===Item table===
 +
Optimizing item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000126    0.000450    YES
 +
RMS    Force            0.000032    0.000300    YES
 +
Maximum Displacement    0.000835    0.001800    YES
 +
RMS    Displacement    0.000219    0.001200    YES
 +
</pre>
 +
 +
Frequency item table
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000126    0.000450    YES
 +
RMS    Force            0.000032    0.000300    YES
 +
Maximum Displacement    0.001285    0.001800    YES
 +
RMS    Displacement    0.000457    0.001200    YES
 +
</pre>
 +
 +
===Optimised molecule image===
 +
[[File:Me3ClNH KATW image.PNG|150px]]
 +
<jmol><jmolApplet>
 +
<title>3D Me3NH Cl molecule</title>
 +
<color>#ff82a8</color>
 +
<size>200</size>
 +
<uploadedFileContents>KATW ME3NH-CLACTUAL.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 +
====Key bond distances and angles====
 +
*add another decimal point to each
 +
{| class="wikitable"
 +
|r(N-C) bond distance|| 1.48&Acirc;
 +
|-
 +
|r(N-H) bond distance|| 0.80&Acirc;
 +
|-
 +
|r(N-Cl) bond distance|| 3.20&Acirc;
 +
|-
 +
|r(C-H) bond distance|| 1.09&Acirc;
 +
|-
 +
| &theta;(C-N-C) bond angle|| 112&deg;
 +
|-
 +
| &theta;(C-N-H) bond angle|| 106&deg;
 +
|-
 +
| &theta;(H-C-H) bond angle|| 110&deg;
 +
|}
 +
 +
===File history===
 +
[[Media:KATW ME3NH-CLACTUAL.LOG]]
 +
 +
 +
 +
===NH<sub>3</sub>BH<sub>3</sub> frequencies===
 +
<pre>
 +
Low frequencies ---  -3.0077  -0.5001  -0.0059  -0.0053  -0.0047    6.2314
 +
Low frequencies ---  81.5384  81.6770  183.6441
 +
</pre>
 +
 +
===NH<sub>3</sub>BH<sub>3</sub> scan of total energy===
 +
 +
<b>Snapshot: </b>
 +
 +
X-Axis:  Scan Coordinate <p>
 +
</p>Y-Axis:  Total Energy (Hartree)
 +
                  X                  Y
 +
        0.8000000000    -635.2162861320
 +
        0.9000000000    -635.2709452560
 +
        1.0000000000    -635.2930688430
 +
        1.1000000000    -635.2992906270
 +
        1.2000000000    -635.2988745370
 +
        1.3000000000    -635.2968157070
 +
        1.4000000000    -635.2956086330
 +
        1.5000000000    -635.2962523740
 +
        1.6000000000    -635.2987711990
 +
        1.7000000000    -635.3023546920
 +
        1.8000000000    -635.3052254510
 +
        1.9000000000    -635.3042681400
 +
        2.0000000000    -635.2943300920
 +
        2.1000000000    -635.2670421330
 +
 +
<b>Scan of the potential energy surface original graph:</b>
 +
 +
[[File:KATW MeNHCl scan graph1.PNG|350px]]
 +
 +
==Relative energies==
 +
 +
{| class="wikitable"
 +
|molecule||Energy (au)||Energy (kJ/mol)||3||4||5||6
 +
|-
 +
|NH3||-56.557769||-148492||1213||2583||2716||2716
 +
|-
 +
|BH3||-26.615324||-69879||E||A1||E||E
 +
|-
 +
|NH3BH3||-83.2246894||-218506||14||0||126||126
 +
|}
 +
 +
 +
E(NH3BH3)=
 +
 +
== BH<sub>3</sub> molecule ==
 +
===Calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file|| BH3_optimization_KATW.log
 +
|-
 +
|molecule|| BH<sub>3</sub>
 +
|-
 +
|method|| RB3LYP
 +
|-
 +
|basis set|| 6-31G(d,p)
 +
|-
 +
|final energy|| -26.615324au
 +
|-
 +
|RMS gradient||2.114e-06au/bohr
 +
|-
 +
|point group|| D3H
 +
|}
 +
 +
===Item table===
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000004    0.000015    YES
 +
RMS    Force            0.000003    0.000010    YES
 +
Maximum Displacement    0.000017    0.000060    YES
 +
RMS    Displacement    0.000011    0.000040    YES
 +
</pre>
 +
 +
 +
===Optimised molecule image===
 +
[[File:KATW BH3 optimagemol.PNG|150px]]
 +
<jmol><jmolApplet>
 +
<title>3D BH<sub>3</sub> molecule</title>
 +
<color>#ff82a8</color>
 +
<size>200</size>
 +
<uploadedFileContents>BH3 OPTIMIZATION KATW.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 +
====Key bond distances and angles====
 +
{| class="wikitable"
 +
|r(B-H) bond distance|| 1.19&Acirc;
 +
|-
 +
| &theta;(H-B-H) bond angle|| 120&deg;
 +
|}
 +
 +
 +
===File history===
 +
[[Media:BH3 OPTIMIZATION KATW.LOG]]
 +
 +
 +
 +
===BH<sub>3</sub> IR spectrum===
 +
[[File:KATW BH3 IR.PNG]]
 +
 +
===BH<sub>3</sub> frequencies===
 +
<pre>
 +
Low frequencies ---  -11.6940  -11.6861  -6.5543  -0.0006    0.0280    0.4289
 +
Low frequencies --- 1162.9745 1213.1390 1213.1392
 +
</pre>
 +
 +
{| class="wikitable"
 +
|mode||1||2||3||4||5||6
 +
|-
 +
|wavenumber (cm<sup>-1</sup>)||1163||1213||1213||2583||2716||2716
 +
|-
 +
|symmetry||A2||E||E||A1||E||E
 +
|-
 +
|intensity||93||14||14||0||126||126
 +
|}
 +
 +
== NH<sub>3</sub>BH<sub>3</sub> molecule ==
 +
===Calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file|| KATW_NH3BH3_opt.log
 +
|-
 +
|molecule|| NH<sub>3</sub>BH<sub>3</sub>
 +
|-
 +
|method|| RB3LYP
 +
|-
 +
|basis set|| 6-31G(d,p)
 +
|-
 +
|final energy|| -83.2246894au
 +
|-
 +
|RMS gradient||1.264e-06au/bohr
 +
|-
 +
|point group|| C1
 +
|}
 +
 +
===Item table===
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000002    0.000015    YES
 +
RMS    Force            0.000001    0.000010    YES
 +
Maximum Displacement    0.000016    0.000060    YES
 +
RMS    Displacement    0.000007    0.000040    YES
 +
</pre>
 +
 +
 +
===Optimised molecule image===
 +
[[File:KATW NH3BH3 image.PNG|150px]]
 +
<jmol><jmolApplet>
 +
<title>3D BH<sub>3</sub> molecule</title>
 +
<color>#ff82a8</color>
 +
<size>200</size>
 +
<uploadedFileContents>KATW NH3BH3 OPT.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 +
====Key bond distances and angles====
 +
{| class="wikitable"
 +
|r(N-H) bond distance|| 1.02&Acirc;
 +
|-
 +
|r(B-H) bond distance|| 1.21&Acirc;
 +
|-
 +
| &theta;(H-N-H) bond angle|| 108&deg;
 +
|-
 +
| &theta;(H-B-H) bond angle|| 114&deg;
 +
|-
 +
| &theta;(H-B-N) bond angle|| 105&deg;
 +
|-
 +
| &theta;(H-N-B) bond angle|| 111&deg;
 +
|}
 +
 +
 +
===File history===
 +
[[Media:KATW NH3BH3 OPT.LOG]]
 +
 +
 +
 +
 +
===NH<sub>3</sub>BH<sub>3</sub> frequencies===
 +
<pre>
 +
Low frequencies ---  -2.7658  -2.2718  -0.0013  -0.0013  -0.0010    2.9530
 +
Low frequencies ---  263.4333  632.9750  638.4461
 +
</pre>
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
==Lab1 Marking==
 +
It's good that you have a working wiki. However, data in your item table don't match the values in the log file, and you have missed to include the torsion angle. If you have any queries, please contact Prof. Hunt.
 +
 
== NH<sub>3</sub> molecule ==
 
== NH<sub>3</sub> molecule ==
 
===Calculation data===
 
===Calculation data===
Line 10: Line 460:
 
|basis set|| 6-31G(d,p)
 
|basis set|| 6-31G(d,p)
 
|-
 
|-
−
|final energy|| -56.557769
+
|final energy|| -56.557769au
 
|-
 
|-
−
|RMS gradient||1.53e-07
+
|RMS gradient||1.53e-07au/bohr
 
|-
 
|-
 
|point group|| C3v
 
|point group|| C3v
Line 26: Line 476:
 
</pre>
 
</pre>
  
−
===Key bond distances and angles===
+
===Optimised molecule image===
 +
[[File:KATW nh3opt1finalimage.png|150px]]
 +
<jmol><jmolApplet>
 +
<title>3D NH<sub>3</sub> molecule</title>
 +
<color>#ff82a8</color>
 +
<size>200</size>
 +
<uploadedFileContents>KATW307 NH3OPT1.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
====Key bond distances and angles====
 
{| class="wikitable"
 
{| class="wikitable"
 
|r(N-H) bond distance|| 1.02&Acirc;
 
|r(N-H) bond distance|| 1.02&Acirc;
Line 32: Line 490:
 
| &theta;(H-N-H) bond angle|| 106&deg;
 
| &theta;(H-N-H) bond angle|| 106&deg;
 
|}
 
|}
−
 
−
===Optimised molecule image===
 
−
[[File:KATW nh3opt1finalimage.png|150px]]
 
  
 
===File history===
 
===File history===
 
[[Media:KATW307 NH3OPT1.LOG]]
 
[[Media:KATW307 NH3OPT1.LOG]]
  
−
<jmol><jmolApplet>
+
===NH<sub>3</sub> IR spectrum===
−
<title>3D NH<sub>3</sub> molecule</title>
+
[[File:Katw NH3 irphoto.PNG]]
−
<color>#ff82a8</color>
 
−
<size>200</size>
 
−
<uploadedFileContents>KATW307 NH3OPT1.LOG</uploadedFileContents>
 
−
</jmolApplet></jmol>
 
  
 +
===NH<sub>3</sub> frequencies===
 
<pre>
 
<pre>
 
  Low frequencies ---  -5.6864  -3.6131  -3.6124    0.0022    0.0047    0.0163
 
  Low frequencies ---  -5.6864  -3.6131  -3.6124    0.0022    0.0047    0.0163
Line 52: Line 504:
  
 
{| class="wikitable"
 
{| class="wikitable"
−
|mode||1||2||3||4||5
+
|mode||1||2||3||4||5||6
 
|-
 
|-
 
|wavenumber (cm<sup>-1</sup>)||1089||1694||1694||3461||3590||3590
 
|wavenumber (cm<sup>-1</sup>)||1089||1694||1694||3461||3590||3590
Line 71: Line 523:
 
|}
 
|}
  
−
===NH<sub>3</sub> IR spectrum===
 
−
[[File:Katw NH3 irphoto.PNG]]
 
  
−
== Project molecule ==
+
 
 +
== N<sub>2</sub>F<sub>2</sub> molecule==
  
 
===Calculation data===
 
===Calculation data===
Line 86: Line 537:
 
|basis set|| 6-31G(d,p)
 
|basis set|| 6-31G(d,p)
 
|-
 
|-
−
|final energy|| -309.0124
+
|final energy|| -309.0124au
 
|-
 
|-
−
|RMS gradient||1.218e-06
+
|RMS gradient||1.218e-06au/bohr
 
|-
 
|-
 
|point group|| C2v
 
|point group|| C2v
Line 102: Line 553:
 
</pre>
 
</pre>
  
−
===Key bond distances and angles===
+
===Optimised molecule image===
 +
[[File:KATW n2f2opt1image.PNG|150px]]
 +
<jmol><jmolApplet>
 +
<title>3D NH<sub>3</sub> molecule</title>
 +
<color>#ff82a8</color>
 +
<size>200</size>
 +
<uploadedFileContents>KATW307 N2F2OPT1.log</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
====Key bond distances and angles====
 
{| class="wikitable"
 
{| class="wikitable"
 
|r(N-N) bond distance|| 1.22&Acirc;
 
|r(N-N) bond distance|| 1.22&Acirc;
Line 110: Line 569:
 
| &theta;(N-N-F) bond angle|| 114&deg;
 
| &theta;(N-N-F) bond angle|| 114&deg;
 
|}
 
|}
−
 
−
===Optimised molecule image===
 
−
[[File:KATW n2f2opt1image.PNG|150px]]
 
  
 
===File history===
 
===File history===
 
[[Media:KATW307 N2F2OPT1.log]]
 
[[Media:KATW307 N2F2OPT1.log]]
  
−
===N<sub>2</sub>F<sub>2</sub> frequencies===
 
  
−
<jmol><jmolApplet>
+
===N<sub>2</sub>F<sub>2</sub> IR spectrum===
−
<title>3D NH<sub>3</sub> molecule</title>
+
[[File:KATW n2f2IR.PNG]]
−
<color>#ff82a8</color>
 
−
<size>200</size>
 
−
<uploadedFileContents>KATW307 N2F2OPT1.log</uploadedFileContents>
 
−
</jmolApplet></jmol>
 
  
 +
===N<sub>2</sub>F<sub>2</sub> frequencies===
 
<pre>
 
<pre>
 
  Low frequencies ---  -0.0011    0.0008    0.0019    3.4929    4.3715    5.1621
 
  Low frequencies ---  -0.0011    0.0008    0.0019    3.4929    4.3715    5.1621
Line 151: Line 603:
 
|}
 
|}
  
−
===N<sub>2</sub>F<sub>2</sub> IR spectrum===
+
==Questions and answers==
−
[[File:KATW n2f2IR.PNG]]
+
 
 +
<b>1. The molecule from the log file does not have bonds between the F and N atoms, what is going on here?</b>
 +
 
 +
The program running the optimization works under an assumption of what the length of the F and N atoms should be, and since the optimization put their bond length as longer than this assumed value, the program did not include a bond there. As the atoms get closer the program will include a bond between the atoms.
 +
 
 +
<b>2. For your IR analysis how many vibrations are expected from the 3N-6 rule?</b>
 +
 
 +
3N-6 where N is the number of atoms would give N=4 and 3(4)-6= 6 vibrational modes, this is consistent with the number of vibrational modes obtained in the optimization as well.
 +
 
 +
<b>3. Why are there only 4 peaks in the IR spectrum?</b>
  
 +
The A1 vibrational mode at 348 cm<sup>-1</sup> and the A2 vibrational mode at 561 cm<sup>-1</sup> both have an intensity of close to zero and were not detected by the IR
  
−
===Questions and answers===
+
<b>4. For your IR analysis which vibration is the asymmetric N-F stretch?</b>
  
−
1. The molecule from the log file does not have bonds between the F and N atoms, what is going on here?
+
Vibrational mode 3
  
−
The program running the optimization works under an assumption of what the length of the F and N atoms should be, and since the optimization put their bond length as longer than this assumed value, the program did not include a bond there. As the atoms get closer the program will include a bond between the atoms.
+
<b>5. For your IR analysis what is the nature of the highest energy vibration?</b>
  
−
2. For your IR analysis how many vibrations are expected from the 3N-6 rule?
+
Symmetrical N-N bond stretching, vibrational mode 6
  
−
3N-6 where N is the number of atoms would give N=4 and 3(4)-6= 6 vibrational modes, this is consistent with the number of vibrational modes obtained in the optimization as well.
+
<b>6. Which MOs are core orbital MOs? </b>
  
−
3. Why are there only 4 peaks in the IR spectrum?
+
The 1-4 molecular orbitals which are only tied to their respective nuclei and not involved in bonding
  
−
The A1 vibrational mode at and the  
+
<b>7. Provide a picture of MO 9 and beside it the LCAO diagram</b>
  
−
4. For your IR analysis which vibration is the asymmetric N-F stretch?
+
[[File:KATW n2f2mol9.PNG]] [[File:LCAO KATW.png|450px]]
−
5. For your IR analysis what is the nature of the highest energy vibration?
 

Latest revision as of 05:00, 15 May 2026

to do

  • redo some of the accuracies

tabulate and compare all the H---Cl distances for all ion-pairs. how do the H-bonds of Me3NH and HMim compare? how do the H-bonds of the N-H and C-H H-bonds compare? are these distances representative of a H-bond? Hint compare your distances to the sum of the van der waals radii of H and Cl. will the ionic nature of the ions effect a distance based assessment of H-bonding? provide a table and comparison of the association energy for a-c make this explicit, so give the energy of each component in atomic units, compute the deltaE in au and then convert to kJ/mol provide the relative energy of the two isomers (a) and (b), ask if you are not sure what this is. rationalise why one conformer is less stable than the other. discuss the dissociation energy of (c) relative to (a) and (b). What does the comparison tell us about the H-bonding? scan the N-H coordinate towards Cl of (a) take your optimised (a)structure, swap atoms to make N=1 and H=2, set the N-H distance to 0.8 and the N-Cl distance to 3.2, run the scan. This will take some time, start it early! provide a snapshot from gaussview of the "raw" HMim-Cl PES plot provide a chemical diagram of the two protonation states for HMim-Cl graph the MeNH-Cl and HMim-Cl scans on a single PES plot discuss your HMim-Cl PES plot, compare and contrast your results for the MeNH-Cl and HMim-Cl PES.

1-methyl-imidazolium chloride

Calculation data

name of submitted log file KATW_RINGA_OPTFREQ2.log
molecule 1-methyl-imidazolium chloride A
method RB3LYP
basis set 3-21G
final energy -722.68731au
RMS gradient 5.198e-06au/bohr
point group C1


Item table

Optimizing item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000011     0.000450     YES
 RMS     Force            0.000003     0.000300     YES
 Maximum Displacement     0.001137     0.001800     YES
 RMS     Displacement     0.000246     0.001200     YES

Frequency item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000011     0.000450     YES
 RMS     Force            0.000003     0.000300     YES
 Maximum Displacement     0.001332     0.001800     YES
 RMS     Displacement     0.000305     0.001200     YES


Key bond distances and angles

  • add another decimal point to each
r(H-Cl) bond distance 1.719Â

File history

Media:KATW RINGA OPTFREQ2.LOG


1-methyl-imidazolium chloride A frequencies

 Low frequencies ---   -5.2962   -2.8134   -0.0015    0.0024    0.0026    2.7809
 Low frequencies ---   36.1361   64.4953   80.8261

The initial frequency scan resulted in a negative frequency vibration from the methyl group. The methyl group was manually rotated and the scan run again with reading internal force constants to yield better data.

Calculation data

name of submitted log file KATW RINGB OPTFREQ2.LOG
molecule 1-methyl-imidazolium chloride B
method RB3LYP
basis set 3-21G
final energy -722.6662au
RMS gradient 2.5631e-05au/bohr
point group C1


Item table

Optimizing item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000088     0.000450     YES
 RMS     Force            0.000020     0.000300     YES
 Maximum Displacement     0.000693     0.001800     YES
 RMS     Displacement     0.000163     0.001200     YES

Frequency item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000088     0.000450     YES
 RMS     Force            0.000020     0.000300     YES
 Maximum Displacement     0.001343     0.001800     YES
 RMS     Displacement     0.000321     0.001200     YES


Key bond distances and angles

  • add another decimal point to each
r(CH-Cl) bond distance 2.134Â
r(CH2H-Cl) bond distance 2.277Â

File history

Media:KATW RINGB OPTFREQ2.LOG


1-methyl-imidazolium chloride B frequencies

 Low frequencies ---   -6.2380   -3.1641    0.0011    0.0033    0.0040    1.3698
 Low frequencies ---   45.3380  162.1734  198.8517


Calculation data

name of submitted log file KATW_RINGC_OPTFREQ.log
molecule 1-methyl-imidazolium chloride C
method RB3LYP
basis set 3-21G
final energy -761.77953au
RMS gradient 8.305e-06au/bohr
point group C1


Item table

Optimizing item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000027     0.000450     YES
 RMS     Force            0.000005     0.000300     YES
 Maximum Displacement     0.000555     0.001800     YES
 RMS     Displacement     0.000154     0.001200     YES

Frequency item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000027     0.000450     YES
 RMS     Force            0.000005     0.000300     YES
 Maximum Displacement     0.000581     0.001800     YES
 RMS     Displacement     0.000167     0.001200     YES


Key bond distances and angles

r(H-Cl) bond distance 2.030Â

File history

Media:KATW RINGC OPTFREQ.LOG


1-methyl-imidazolium chloride C frequencies

 Low frequencies ---   -3.7052   -3.0699   -0.0042   -0.0027   -0.0019    2.2969
 Low frequencies ---   52.1621  102.5835  107.1578


Me3NH Cl molecule

Calculation data

name of submitted log file KATW_Me3NH-Clactual.log
molecule Me3NH Cl
method RB3LYP
basis set 6-31G(d,p)
final energy -635.31113au
RMS gradient 4.0214e-05au/bohr
point group C1

The above point group was not set to be C3v, which it should be, so the program assigned it C1.

Item table

Optimizing item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000126     0.000450     YES
 RMS     Force            0.000032     0.000300     YES
 Maximum Displacement     0.000835     0.001800     YES
 RMS     Displacement     0.000219     0.001200     YES

Frequency item table 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000126     0.000450     YES
 RMS     Force            0.000032     0.000300     YES
 Maximum Displacement     0.001285     0.001800     YES
 RMS     Displacement     0.000457     0.001200     YES

Optimised molecule image

Me3ClNH KATW image.PNG

3D Me3NH Cl molecule

Key bond distances and angles

  • add another decimal point to each
r(N-C) bond distance 1.48Â
r(N-H) bond distance 0.80Â
r(N-Cl) bond distance 3.20Â
r(C-H) bond distance 1.09Â
θ(C-N-C) bond angle 112°
θ(C-N-H) bond angle 106°
θ(H-C-H) bond angle 110°

File history

Media:KATW ME3NH-CLACTUAL.LOG


NH3BH3 frequencies

 Low frequencies ---   -3.0077   -0.5001   -0.0059   -0.0053   -0.0047    6.2314
 Low frequencies ---   81.5384   81.6770  183.6441

NH3BH3 scan of total energy

Snapshot:

X-Axis: Scan Coordinate

Y-Axis: Total Energy (Hartree) 

                 X                   Y
       0.8000000000     -635.2162861320
       0.9000000000     -635.2709452560
       1.0000000000     -635.2930688430
       1.1000000000     -635.2992906270
       1.2000000000     -635.2988745370
       1.3000000000     -635.2968157070
       1.4000000000     -635.2956086330
       1.5000000000     -635.2962523740
       1.6000000000     -635.2987711990
       1.7000000000     -635.3023546920
       1.8000000000     -635.3052254510
       1.9000000000     -635.3042681400
       2.0000000000     -635.2943300920
       2.1000000000     -635.2670421330

Scan of the potential energy surface original graph:

KATW MeNHCl scan graph1.PNG

Relative energies

molecule Energy (au) Energy (kJ/mol) 3 4 5 6
NH3 -56.557769 -148492 1213 2583 2716 2716
BH3 -26.615324 -69879 E A1 E E
NH3BH3 -83.2246894 -218506 14 0 126 126


E(NH3BH3)=

BH3 molecule

Calculation data

name of submitted log file BH3_optimization_KATW.log
molecule BH3
method RB3LYP
basis set 6-31G(d,p)
final energy -26.615324au
RMS gradient 2.114e-06au/bohr
point group D3H

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000004     0.000015     YES
 RMS     Force            0.000003     0.000010     YES
 Maximum Displacement     0.000017     0.000060     YES
 RMS     Displacement     0.000011     0.000040     YES


Optimised molecule image

KATW BH3 optimagemol.PNG

3D BH molecule

Key bond distances and angles

r(B-H) bond distance 1.19Â
θ(H-B-H) bond angle 120°


File history

Media:BH3 OPTIMIZATION KATW.LOG


BH3 IR spectrum

KATW BH3 IR.PNG

BH3 frequencies

 Low frequencies ---  -11.6940  -11.6861   -6.5543   -0.0006    0.0280    0.4289
 Low frequencies --- 1162.9745 1213.1390 1213.1392
mode 1 2 3 4 5 6
wavenumber (cm-1) 1163 1213 1213 2583 2716 2716
symmetry A2 E E A1 E E
intensity 93 14 14 0 126 126

NH3BH3 molecule

Calculation data

name of submitted log file KATW_NH3BH3_opt.log
molecule NH3BH3
method RB3LYP
basis set 6-31G(d,p)
final energy -83.2246894au
RMS gradient 1.264e-06au/bohr
point group C1

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000016     0.000060     YES
 RMS     Displacement     0.000007     0.000040     YES


Optimised molecule image

KATW NH3BH3 image.PNG

3D BH molecule

Key bond distances and angles

r(N-H) bond distance 1.02Â
r(B-H) bond distance 1.21Â
θ(H-N-H) bond angle 108°
θ(H-B-H) bond angle 114°
θ(H-B-N) bond angle 105°
θ(H-N-B) bond angle 111°


File history

Media:KATW NH3BH3 OPT.LOG



NH3BH3 frequencies

 Low frequencies ---   -2.7658   -2.2718   -0.0013   -0.0013   -0.0010    2.9530
 Low frequencies ---  263.4333  632.9750  638.4461





Lab1 Marking

It's good that you have a working wiki. However, data in your item table don't match the values in the log file, and you have missed to include the torsion angle. If you have any queries, please contact Prof. Hunt.

NH3 molecule

Calculation data

name of submitted log file KATW307_nh3opt1.log
molecule NH3
method RB3LYP
basis set 6-31G(d,p)
final energy -56.557769au
RMS gradient 1.53e-07au/bohr
point group C3v

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000010     0.000060     YES
 RMS     Displacement     0.000006     0.000040     YES

Optimised molecule image

KATW nh3opt1finalimage.png

3D NH molecule

Key bond distances and angles

r(N-H) bond distance 1.02Â
θ(H-N-H) bond angle 106°

File history

Media:KATW307 NH3OPT1.LOG

NH3 IR spectrum

Katw NH3 irphoto.PNG

NH3 frequencies

 Low frequencies ---   -5.6864   -3.6131   -3.6124    0.0022    0.0047    0.0163
 Low frequencies --- 1089.3674 1693.9284 1693.9284
mode 1 2 3 4 5 6
wavenumber (cm-1) 1089 1694 1694 3461 3590 3590
symmetry A1 E E A1 E E
intensity 145 14 14 1 0 0

NH3 charges

Katw nh3 chargemapfinal.PNG

Atom Charge (e)
N -1.13
H3 0.38


N2F2 molecule

Calculation data

name of submitted log file KATW307_n2f2opt1.log
molecule N2F2
method RB3LYP
basis set 6-31G(d,p)
final energy -309.0124au
RMS gradient 1.218e-06au/bohr
point group C2v

Item table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000000     0.000015     YES
 RMS     Force            0.000000     0.000010     YES
 Maximum Displacement     0.000003     0.000060     YES
 RMS     Displacement     0.000001     0.000040     YES

Optimised molecule image

KATW n2f2opt1image.PNG

3D NH molecule

Key bond distances and angles

r(N-N) bond distance 1.22Â
r(N-F) bond distance 1.39Â
θ(N-N-F) bond angle 114°

File history

Media:KATW307 N2F2OPT1.log


N2F2 IR spectrum

KATW n2f2IR.PNG

N2F2 frequencies

 Low frequencies ---   -0.0011    0.0008    0.0019    3.4929    4.3715    5.1621
 Low frequencies ---  347.8732  561.2460  771.6039
mode 1 2 3 4 5 6
wavenumber (cm-1) 348 561 772 949 987 1637
symmetry A1 A2 B2 A1 B2 A1
intensity (arbitrary units) 1 0 75 75 81 21

N2F2 charges

KATW n2f2opt1chargemap.PNG

Atom Charge (e)
N2 0.22
F2 -0.22

Questions and answers

1. The molecule from the log file does not have bonds between the F and N atoms, what is going on here?

The program running the optimization works under an assumption of what the length of the F and N atoms should be, and since the optimization put their bond length as longer than this assumed value, the program did not include a bond there. As the atoms get closer the program will include a bond between the atoms.

2. For your IR analysis how many vibrations are expected from the 3N-6 rule?

3N-6 where N is the number of atoms would give N=4 and 3(4)-6= 6 vibrational modes, this is consistent with the number of vibrational modes obtained in the optimization as well.

3. Why are there only 4 peaks in the IR spectrum?

The A1 vibrational mode at 348 cm-1 and the A2 vibrational mode at 561 cm-1 both have an intensity of close to zero and were not detected by the IR

4. For your IR analysis which vibration is the asymmetric N-F stretch?

Vibrational mode 3

5. For your IR analysis what is the nature of the highest energy vibration?

Symmetrical N-N bond stretching, vibrational mode 6

6. Which MOs are core orbital MOs?

The 1-4 molecular orbitals which are only tied to their respective nuclei and not involved in bonding

7. Provide a picture of MO 9 and beside it the LCAO diagram

KATW n2f2mol9.PNG LCAO KATW.png

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