Difference between revisions of "Milmindani"

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==Lab1 Marking==
 
==Lab1 Marking==
−
It's good that you have a working wiki. However, your reported image and charges of N2F2 do not correspond to an optimised structure. Don't forget to consider the accuracy to which you report your data the next time. If you have any queries, please contact Prof. Hunt.  
+
It's good that you have a working wiki. However, your reported image and charges of N2F2 do not correspond to an optimised structure. Don't forget to consider the accuracy to which you report your data the next time. If you have any queries, please contact Prof. Hunt.
 +
==Lab2 Marking==
 +
It's good that you have a working wiki. However, in optimising Me3NH+...Cl-, you used a wrong basis set, data in your item table don't match the values in the log file, item table from the opt job and low frequencies are not reported in your wiki, and distances are incorrect. You missed to include raw PES and explanation of the scanned coordinate and used hartree in your report quality PES graph. It would be good if you uploaded all the log files for the project molecule and rounded off values to correct dp. If you have any queries, please contact Prof. Hunt.
 +
 
 +
== Observations ==
 +
 
 +
Friday 2:45pm: The computers failed to run jobs to optimize and check the frequency of the HMim-Cl Molecule many times. This probably occurred over 10-15 times. I have retried over and over again and it has been unsuccessful so far.
 +
Friday 3:00pm: Molecule B Optimised.
 +
Friday 3:30pm: Still trouble with optimising A and C. Changed methyl groups angle on A. Made sure no spaces in names and saved in D Drive.
 +
Friday 3:45pm: Molecule A Optimised.
 +
Friday: 4:15: Molecule C Optimised.
 +
Friday: 4:30: Answers half completed but ran out of time to finalize the rest of the questions and discussion.
 +
 
 +
== Question Answers and Tabulation ==
 +
 
 +
<b>Tabulate and compare all the H---Cl distances for all ion-pairs.</b>
 +
 
 +
Molecule A
 +
Bond Distance: r(H-Cl)=1.71993&Acirc;<br>
 +
Molecule B
 +
Bond Distance: r(H-Cl)=2.13353&Acirc;<br>
 +
Molecule C
 +
Bond Distance: r(H-Cl)=2.13353&Acirc;<br>
 +
 
 +
Molecule A has an H-Cl in line and in close proximity to each other and is relatively close at 1.71993&Acirc<br>
 +
Molecule B the closest H-CL is further away as the Cl is floating in solution further away at 2.13353&Acirc<br>
 +
Molecule C  H-CL is further away as the Cl is floating in solution further away at 2.13353&Acirc<br>
 +
 
 +
<b>how do the H-bonds of Me3NH and HMim compare?</b><br>
 +
Me3NH-Cl Optimised bond distance <br>
 +
Bond Distance: r(N-H)=1.16186Â<br>
 +
Bond Distance: r(N-Cl)=2.90049Â<br>
 +
Bond Distance: r(CH3-H)=1.09119&Acirc;<br>
 +
 
 +
 
 +
Compared to Molecule B of HMim-Cl<br>
 +
Optimised bond distance and angle for HMim-Cl<br>
 +
Bond Distance: r(N-H)=1.01395Â<br>
 +
Bond Distance: r(N-CH3)=1.49638Â<br>
 +
Bond Distance: r(N-Cl)=3.14742Â<br>
 +
Bond Distance: r(CH3-H)=1.09126&Acirc;<br>
 +
Bond Distance: r(CH-H)=1.07474&Acirc;<br>
 +
 
 +
The N-CL bond is longer in HMim-Cl compared to Me3NH-Cl by 0.24693Â. <br>
 +
The N-H bond is shorter in HMim-Cl compared to Me3NH-Cl by 0.14791Â.<br>
 +
 
 +
<b>how do the H-bonds of the N-H and C-H H-bonds compare?</b><br>
 +
The N-H bond is shorter in HMim-Cl compared to Me3NH-Cl by 0.14791Â.<br>
 +
The CH<sub>3</sub>-H bond is pretty much the same in HMim-Cl compared to Me3NH-Cl<br>
 +
The C-H bond in HMim-Cl is 1.07474&Acirc; there are no C-H bonds in Me3NH-Cl<br>
 +
 
 +
<b>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.</b><br>
 +
The standard H-Bond is 1.0&Acirc; Our H-Bonds are slightly longer at 1.07-1.16&Acirc;
 +
https://bc401.bmb.colostate.edu/appendix/h-bonds.php
 +
 
 +
<b>will the ionic nature of the ions effect a distance based assessment of H-bonding?</b><br>
 +
Yes. The proton will be attracted to the negative Cl Ion.
 +
 
 +
 
 +
Discussion Continued:
 +
<br>
 +
<b>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</b><br>
 +
 
 +
<br>
 +
<b>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.</b><br>
 +
 
 +
<br>
 +
<b>discuss the dissociation energy of (c) relative to (a) and (b). What does the comparison tell us about the H-bonding?</b><br>
 +
<br>
 +
<b>scan the N-H coordinate towards Cl of (a)</b><br>
 +
<br>
 +
<b>provide a snapshot from gaussview of the "raw" HMim-Cl PES plot</b><br>
 +
<br>
 +
<b>provide a chemical diagram of the two protonation states for HMim-Cl</b><br>
 +
<br>
 +
<b>graph the MeNH-Cl and HMim-Cl scans on a single PES plot</b><br>
 +
<br>
 +
<b>discuss your HMim-Cl PES plot, compare and contrast your results for the MeNH-Cl and HMim-Cl PES.
 +
discuss means we are asking for some interpretation of your results. Students have a tendency to simply describe the data (do not do this!), we can see the data in the tables, make sure you are interpreting the data or adding new information. For example if the association a A is more stabilising than B, evaluate the difference and give the energy, provide a potential rationalisation of why this might occur, even better if you can suggest a way of testing your hypothesis!</b><br>
 +
 
 +
 
 +
 
 +
== d.) Cl- Molecule Optimised Version ==
 +
 
 +
{| class="wikitable"
 +
|name of submitted log file || DM CLMINUS.LOG
 +
|-
 +
|molecule || Cl-
 +
|-
 +
|method || B3LYP
 +
|-
 +
|Calculation Type || SP
 +
|-
 +
|calculation method || RB3LYP
 +
|-
 +
|basis set || 3-21G
 +
|-
 +
|charge|| -1
 +
|-
 +
|RMS gradient || 0.000000
 +
|-
 +
|point group || OH
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
[[File:CL-Molecule-Image-DM.PNG|450px]]
 +
 
 +
[[Media:DM CLMINUS.LOG]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image BH<sub>3</sub></title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>DM CLMINUS.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
 
 +
== c.) HMim-Cl Molecule Optimised Version ==
 +
 
 +
{| class="wikitable"
 +
|name of submitted log file || C HMim CL OPTIMISATION.log
 +
|-
 +
|molecule || HMim-Cl (C<sub>4</sub>H<sub>7</sub>ClN<sub>2</sub>)
 +
|-
 +
|method || B3LYP
 +
|-
 +
|Calculation Type || FREQ
 +
|-
 +
|calculation method || RB3LYP
 +
|-
 +
|basis set || 3-21G
 +
|-
 +
|final energy||
 +
|-
 +
|RMS gradient ||
 +
|-
 +
|point group || C1
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
 
 +
[[File:C-HMim-CL-Molecule Image DM.PNG|450px]]
 +
 
 +
[[Media:C HMim CL OPTIMISATION.log]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image HMim-CL</title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>C HMim CL OPTIMISATION.log</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
===Bond Distances===
 +
Optimised bond distance and angle for  Me<sub>3</sub>NH-Cl<br>
 +
Bond Distance: r(N-CH<sub>3</sub>)=1.49020&Acirc;<br>
 +
Bond Distance: r(N-Cl)=3.66576&Acirc;<br>
 +
Bond Distance: r(C-H)=1.11784&Acirc;<br>
 +
 
 +
===Item Table===
 +
<pre>
 +
          Item              Value    Threshold  Converged?
 +
Maximum Force            0.000008    0.000450    YES
 +
RMS    Force            0.000002    0.000300    YES
 +
Maximum Displacement    0.001826    0.001800    NO
 +
RMS    Displacement    0.000274    0.001200    YES
 +
</pre>
 +
 
 +
 
 +
 
 +
== b.) HMim-Cl Molecule Optimised Version ==
 +
 
 +
{| class="wikitable"
 +
|name of submitted log file || B-HMIM-CL-OPTIMISATION.LOG
 +
|-
 +
|molecule || HMim-Cl (C<sub>4</sub>H<sub>7</sub>ClN<sub>2</sub>)
 +
|-
 +
|Calculation Type || FREQ
 +
|-
 +
|method || B3LYP
 +
|-
 +
|calculation method || RB3LYP
 +
|-
 +
|basis set || 3-21G
 +
|-
 +
|final energy|| -722.666200
 +
|-
 +
|RMS gradient || 0.000014
 +
|-
 +
|point group || C1
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
 
 +
[[File:B-HMim-CL-Molecule-Image-DM.PNG|450px]]
 +
 
 +
[[Media:B-HMIM-CL-OPTIMISATION.LOG]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image BH<sub>3</sub></title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>B-HMIM-CL-OPTIMISATION.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
===Bond Distances===
 +
Optimised bond distance and angle for  Me<sub>3</sub>NH-Cl<br>
 +
Bond Distance: r(N-H)=1.01395&Acirc;<br>
 +
Bond Distance: r(N-CH<sub>3</sub>)=1.49638&Acirc;<br>
 +
Bond Distance: r(N-Cl)=3.64990&Acirc;<br>
 +
Bond Distance: r(H-Cl)=2.13353&Acirc;<br>
 +
 
 +
===Item Table===
 +
<pre>
 +
          Item              Value    Threshold  Converged?
 +
Maximum Force            0.000050    0.000450    YES
 +
RMS    Force            0.000008    0.000300    YES
 +
Maximum Displacement    0.004359    0.001800    NO
 +
RMS    Displacement    0.001247    0.001200    NO
 +
</pre>
 +
== a.) HMim-Cl Molecule Optimised Version ==
 +
 
 +
{| class="wikitable"
 +
|name of submitted log file || A HMIM CL OPTIMISATION.LOG
 +
|-
 +
|molecule || HMim-Cl (C<sub>4</sub>H<sub>7</sub>ClN<sub>2</sub>)
 +
|-
 +
|Calculation Type || FREQ
 +
|-
 +
|method || B3LYP
 +
|-
 +
|calculation method || RB3LYP
 +
|-
 +
|basis set || 3-21G
 +
|-
 +
|final energy|| -722.687898
 +
|-
 +
|RMS gradient || 0.000019
 +
|-
 +
|point group || C1
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
 
 +
[[File:A-HMim-CL-Molecule Image DM.PNG|450px]]
 +
 
 +
[[Media:A HMIM CL OPTIMISATION.LOG]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image BH<sub>3</sub></title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>A HMIM CL OPTIMISATION.LOG</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
===Bond Distances===
 +
Optimised bond distance and angle for  Me<sub>3</sub>NH-Cl<br>
 +
Bond Distance: r(N-H)=1.17721&Acirc;<br>
 +
Bond Distance: r(N-CH<sub>3</sub>)=1.47704&Acirc;<br>
 +
Bond Distance: r(N-Cl)=2.89156&Acirc;<br>
 +
 
 +
 
 +
===Item Table===
 +
<pre>
 +
        Item              Value    Threshold  Converged?
 +
Maximum Force            0.000052    0.000450    YES
 +
RMS    Force            0.000010    0.000300    YES
 +
Maximum Displacement    0.002398    0.001800    NO
 +
RMS    Displacement    0.000450    0.001200    YES
 +
 
 +
</pre>
 +
 
 +
== Me<sub>3</sub>NH-Cl Molecule Optimised Version ==
 +
===Calculation Data===
 +
{| class="wikitable"
 +
|name of submitted log file || DM me3NHCL Optimisation.log
 +
|-
 +
|molecule || Me<sub>3</sub>NH-Cl
 +
|-
 +
|method || FOPT
 +
|-
 +
|calculation method ||
 +
|-
 +
|basis set || 3-21G(d,p)
 +
|-
 +
|final energy|| -632.162045
 +
|-
 +
|RMS gradient || 0.000394
 +
|-
 +
|point group || C1
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
[[File:Me3NHCl Molecule DM.PNG|450px]]
 +
 
 +
[[Media:DM me3NHCL Optimisation.log]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image BH<sub>3</sub></title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>DM me3NHCL Optimisation2.log</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
===Bond Distances===
 +
Optimised bond distance and angle for  Me<sub>3</sub>NH-Cl<br>
 +
Bond Distance: r(N-H)=1.16186&Acirc;<br>
 +
Bond Distance: r(N-Cl)=2.90049&Acirc;<br>
 +
Bond Distance: r(Ch3-H)=1.09119&Acirc;<br>
 +
 
 +
===Item Table===
 +
<pre>
 +
Item              Value    Threshold  Converged?
 +
Maximum Force            0.000942    0.000015    NO
 +
RMS    Force            0.000323    0.000010    NO
 +
Maximum Displacement    0.087442    0.000060    NO
 +
RMS    Displacement    0.014422    0.000040    NO
 +
 
 +
</pre>
 +
 
 +
== Me<sub>3</sub>NH-Cl Molecule Scanned Version ==
 +
===Calculation Data===
 +
{| class="wikitable"
 +
|name of submitted log file || DM me3NHCL RIGID SCAN.log
 +
|-
 +
|molecule || Me<sub>3</sub>NH-Cl
 +
|-
 +
|method || SCAN
 +
|-
 +
|calculation method || RB3LYP
 +
|-
 +
|basis set || 3-21G
 +
|-
 +
|final energy|| -632.066188
 +
|-
 +
|RMS gradient || Blank-No Gradient Listed
 +
|-
 +
|point group || C1
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
[[File:Me3NHCl Molecule Scan DM.PNG|450px]]
 +
 
 +
[[Media:DM me3NHCL RIGID SCAN.log]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image BH<sub>3</sub></title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>DM me3NHCL Optimisation2.log</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
===Bond Distances===
 +
Optimised bond distance and angle for  Me<sub>3</sub>NH-Cl<br>
 +
Bond Distance: r(N-H)=0.80000&Acirc;<br>
 +
Bond Distance: r(N-Cl)=3.20000&Acirc;<br>
 +
 
 +
===Scan of Total Energy===
 +
[[File:Me3NHCl Molecule Scan of Total Energy DM.PNG|600px]]
 +
 
 +
This is the total energy of the scanned molecule. It is a U-Shape. The Raw data is available below for your perusal.
 +
 
 +
[[File:Me3NHCl Scan of Total Energy Data.log|450px]]
 +
 
 +
== Bond Energy Calculations NH<sub>3</sub>BH<sub>3</sub> ==
 +
===Calculation Data===
 +
{| class="wikitable"
 +
|E(NH<sub>3</sub>) || -56.557769 AU
 +
|-
 +
|E(BH<sub>3</sub>) || -26.615324 AU
 +
|-
 +
|E(NH<sub>3</sub>BH<sub>3</sub>) || -83.224689 AU
 +
|-
 +
|ΔE AU) || E(NH3BH3)-[E(NH3)+E(BH3)] = -83.224689 - (-56.557769+-26.615324) = -0.051596AU
 +
|-
 +
|ΔE Kj/mol) || -0.051596AU *  2625.4999 kJ/mol = 1 a.u. = -135.46529284 kJ/mol
 +
|-
 +
|}
 +
 
 +
 
 +
 
 +
 
 +
 
 +
== NH<sub>3</sub>BH<sub>3</sub> Molecule ==
 +
===calculation data===
 +
{| class="wikitable"
 +
|name of submitted log file || NH3BH3_Optimisation_Log_File.log.log
 +
|-
 +
|molecule || NH<sub>3</sub>BH<sub>3</sub>
 +
|-
 +
|method || B3LYP
 +
|-
 +
|calculation method || RB3LYP
 +
|-
 +
|basis set || 6-31G(d,p)
 +
|-
 +
|final energy|| -83.224689
 +
|-
 +
|RMS gradient ||0.000001
 +
|-
 +
|point group || C1
 +
|-
 +
|Confirmed it is Minima || Yes
 +
|}
 +
 
 +
[[File:NH3BH3 Molecule Image.PNG|450px]]
 +
 
 +
[[Media:NH3BH3_Optimisation_Log_File.log.log]]
 +
 
 +
<jmol><jmolApplet>
 +
<title>rotateable 3D Jmol image BH<sub>3</sub></title>
 +
<color>black</color>
 +
<size>200</size>
 +
<uploadedFileContents>NH3BH3_Optimisation_Log_File.log.log</uploadedFileContents>
 +
</jmolApplet></jmol>
 +
 
 +
===Item Table===
 +
<pre>
 +
Item              Value    Threshold  Converged?
 +
Maximum Force            0.000002    0.000015    YES
 +
RMS    Force            0.000001    0.000010    YES
 +
Maximum Displacement    0.000041    0.000060    YES
 +
RMS    Displacement    0.000020    0.000040    YES
 +
 
 +
</pre>
 +
 
 +
===Important geometric parameters===
 +
Optimised bond distance and angle for  BH<sub>3</sub><br>
 +
Bond Distance: r(N-H)=1.01847&Acirc;<br>
 +
Bond Distance: r(B-H)=1.20977&Acirc;<br>
 +
Bond Distance: r(B-N)=1.66771&Acirc;<br>
 +
 
 +
Bond Angle (N-H): 107.88&deg;<br>
 +
Bond Angle (B-H): 113.88&deg;<br>
 +
Low frequencies ---  -3.6199  -0.0014  -0.0010  -0.0009    2.3908    4.5604
 +
Low frequencies ---  263.4365  632.9747  638.4332<br>
 +
 
 +
{| class="wikitable"
 +
|Mode || 1 || 2 || 3 || 4 || 5 || 6 || 7 || 8 || 9 || 10 || 11 || 12 || 13 || 14 || 15 || 16 || 17 || 18 ||
 +
|-
 +
|wavenumber (cm<sub>-1</sub>) || 263.4365 || 632.9747 || 638.4332 || 638.5054 || 1069.1617|| 1069.1617 || 1196.1866|| 1203.5225|| 1203.5771|| 1328.8170|| 1676.0434|| 1676.0577|| 2471.9811|| 2532.0716||  2532.0950|| 3464.1021|| 3581.1459|| 3581.1541 ||
 +
|-
 +
|Symmetry || A || A || A || A || A || A || A || A || A || A || A || A || A || A || A || A || A || A ||
 +
|-
 +
|intensity (arbitrary units) || 0.0000 || 14.0108 || 3.5475 || 3.5464 || 40.5051 || 40.5105 || 108.9677 || 3.4694 || 3.4694 || 113.6226 || 27.5645 || 27.5669 || 67.2027 || 231.2478 || 231.2478 || 2.5113 || 27.9556 || 27.9571 ||
 +
|}
 +
 
 +
[[File:NH3BH3 Molecule Image.PNG|600px]]
 +
[[File:NH3BH3 Molecule Charge Analysis DM.PNG|600px]]
 +
[[File:NH3BH3 Molecule Charge Analysis Legend DM.PNG|300px]]
 +
 
  
 
== BH<sub>3</sub> Molecule ==
 
== BH<sub>3</sub> Molecule ==
−
===calculation data===
+
===Calculation Data===
 
{| class="wikitable"
 
{| class="wikitable"
 
|name of submitted log file || BH3 Optimisation DM.log
 
|name of submitted log file || BH3 Optimisation DM.log
Line 49: Line 505:
 
Bond Distance: r(N-F)=1.19200&Acirc;<br>
 
Bond Distance: r(N-F)=1.19200&Acirc;<br>
 
Bond Angle (N-F): 120&deg;<br>
 
Bond Angle (N-F): 120&deg;<br>
−
Low frequencies ---  -11.6940  -11.6861  -6.5543  -0.0002    0.0280    0.4289
+
Low frequencies ---  -11.6940  -11.6861  -6.5543  -0.0002    0.0280    0.4289<br>
 
Low frequencies --- 1162.9745 1213.1390 1213.1392<br>
 
Low frequencies --- 1162.9745 1213.1390 1213.1392<br>
  
Line 55: Line 511:
 
|Mode || 1 || 2 || 3 || 4 || 5 || 6
 
|Mode || 1 || 2 || 3 || 4 || 5 || 6
 
|-
 
|-
−
|wavenumber (cm<sub>-1</sub>) || 347.8772 || 561.2472 || 771.6105 || 949.4548 || 987.2543|| 1636.6075
+
|wavenumber (cm<sub>-1</sub>) || 1162.9745 || 1213.1390 || 1213.1392 || 2582.5813 || 2715.7180|| 2715.7189
 
|-
 
|-
−
|Symmetry || A<sub>1</sub> || A<sub>2</sub> || B<sub>2</sub> || A<sub>1</sub> || B<sub>2</sub> || A<sub>1</sub>
+
|Symmetry || A<sub>2</sub>" || E' || E' || A<sub>1</sub>' || E' || E'
 
|-
 
|-
−
|intensity (arbitrary units) ||0.6108 || 0.0000||74.7044||75.4125||81.1265||  20.5391
+
|intensity (arbitrary units) ||92.5282 || 14.0550||14.0544||0.0000||126.3320||  126.3260
 
|}
 
|}
  
−
 
+
[[File:BH3 Molecule IR Spectrum DM.PNG|600px]]
−
 
+
[[File:BH3 Molecule Charge Analysis DM.PNG|600px]]
−
 
+
[[File:BH3 Molecule Charge Analysis Legend DM.PNG|300px]]
−
 
 
−
 
 
  
  

Latest revision as of 05:54, 8 June 2026

Lab1 Marking

It's good that you have a working wiki. However, your reported image and charges of N2F2 do not correspond to an optimised structure. Don't forget to consider the accuracy to which you report your data the next time. If you have any queries, please contact Prof. Hunt.

Lab2 Marking

It's good that you have a working wiki. However, in optimising Me3NH+...Cl-, you used a wrong basis set, data in your item table don't match the values in the log file, item table from the opt job and low frequencies are not reported in your wiki, and distances are incorrect. You missed to include raw PES and explanation of the scanned coordinate and used hartree in your report quality PES graph. It would be good if you uploaded all the log files for the project molecule and rounded off values to correct dp. If you have any queries, please contact Prof. Hunt.

Observations

Friday 2:45pm: The computers failed to run jobs to optimize and check the frequency of the HMim-Cl Molecule many times. This probably occurred over 10-15 times. I have retried over and over again and it has been unsuccessful so far. Friday 3:00pm: Molecule B Optimised. Friday 3:30pm: Still trouble with optimising A and C. Changed methyl groups angle on A. Made sure no spaces in names and saved in D Drive. Friday 3:45pm: Molecule A Optimised. Friday: 4:15: Molecule C Optimised. Friday: 4:30: Answers half completed but ran out of time to finalize the rest of the questions and discussion.

Question Answers and Tabulation

Tabulate and compare all the H---Cl distances for all ion-pairs.

Molecule A Bond Distance: r(H-Cl)=1.71993Â
Molecule B Bond Distance: r(H-Cl)=2.13353Â
Molecule C Bond Distance: r(H-Cl)=2.13353Â

Molecule A has an H-Cl in line and in close proximity to each other and is relatively close at 1.71993&Acirc
Molecule B the closest H-CL is further away as the Cl is floating in solution further away at 2.13353&Acirc
Molecule C H-CL is further away as the Cl is floating in solution further away at 2.13353&Acirc

how do the H-bonds of Me3NH and HMim compare?
Me3NH-Cl Optimised bond distance
Bond Distance: r(N-H)=1.16186Â
Bond Distance: r(N-Cl)=2.90049Â
Bond Distance: r(CH3-H)=1.09119Â


Compared to Molecule B of HMim-Cl
Optimised bond distance and angle for HMim-Cl
Bond Distance: r(N-H)=1.01395Â
Bond Distance: r(N-CH3)=1.49638Â
Bond Distance: r(N-Cl)=3.14742Â
Bond Distance: r(CH3-H)=1.09126Â
Bond Distance: r(CH-H)=1.07474Â

The N-CL bond is longer in HMim-Cl compared to Me3NH-Cl by 0.24693Â.
The N-H bond is shorter in HMim-Cl compared to Me3NH-Cl by 0.14791Â.

how do the H-bonds of the N-H and C-H H-bonds compare?
The N-H bond is shorter in HMim-Cl compared to Me3NH-Cl by 0.14791Â.
The CH3-H bond is pretty much the same in HMim-Cl compared to Me3NH-Cl
The C-H bond in HMim-Cl is 1.07474Â there are no C-H bonds in Me3NH-Cl

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.

The standard H-Bond is 1.0Â Our H-Bonds are slightly longer at 1.07-1.16Â

https://bc401.bmb.colostate.edu/appendix/h-bonds.php

will the ionic nature of the ions effect a distance based assessment of H-bonding?
Yes. The proton will be attracted to the negative Cl Ion.


Discussion Continued:
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)

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. discuss means we are asking for some interpretation of your results. Students have a tendency to simply describe the data (do not do this!), we can see the data in the tables, make sure you are interpreting the data or adding new information. For example if the association a A is more stabilising than B, evaluate the difference and give the energy, provide a potential rationalisation of why this might occur, even better if you can suggest a way of testing your hypothesis!


d.) Cl- Molecule Optimised Version

name of submitted log file DM CLMINUS.LOG
molecule Cl-
method B3LYP
Calculation Type SP
calculation method RB3LYP
basis set 3-21G
charge -1
RMS gradient 0.000000
point group OH
Confirmed it is Minima Yes

CL-Molecule-Image-DM.PNG

Media:DM CLMINUS.LOG

rotateable 3D Jmol image BH


c.) HMim-Cl Molecule Optimised Version

name of submitted log file C HMim CL OPTIMISATION.log
molecule HMim-Cl (C4H7ClN2)
method B3LYP
Calculation Type FREQ
calculation method RB3LYP
basis set 3-21G
final energy
RMS gradient
point group C1
Confirmed it is Minima Yes


C-HMim-CL-Molecule Image DM.PNG

Media:C HMim CL OPTIMISATION.log

rotateable 3D Jmol image HMim-CL

Bond Distances

Optimised bond distance and angle for Me3NH-Cl
Bond Distance: r(N-CH3)=1.49020Â
Bond Distance: r(N-Cl)=3.66576Â
Bond Distance: r(C-H)=1.11784Â

Item Table

          Item               Value     Threshold  Converged?
 Maximum Force            0.000008     0.000450     YES
 RMS     Force            0.000002     0.000300     YES
 Maximum Displacement     0.001826     0.001800     NO 
 RMS     Displacement     0.000274     0.001200     YES


b.) HMim-Cl Molecule Optimised Version

name of submitted log file B-HMIM-CL-OPTIMISATION.LOG
molecule HMim-Cl (C4H7ClN2)
Calculation Type FREQ
method B3LYP
calculation method RB3LYP
basis set 3-21G
final energy -722.666200
RMS gradient 0.000014
point group C1
Confirmed it is Minima Yes


B-HMim-CL-Molecule-Image-DM.PNG

Media:B-HMIM-CL-OPTIMISATION.LOG

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me3NH-Cl
Bond Distance: r(N-H)=1.01395Â
Bond Distance: r(N-CH3)=1.49638Â
Bond Distance: r(N-Cl)=3.64990Â
Bond Distance: r(H-Cl)=2.13353Â

Item Table

          Item               Value     Threshold  Converged?
 Maximum Force            0.000050     0.000450     YES
 RMS     Force            0.000008     0.000300     YES
 Maximum Displacement     0.004359     0.001800     NO 
 RMS     Displacement     0.001247     0.001200     NO

a.) HMim-Cl Molecule Optimised Version

name of submitted log file A HMIM CL OPTIMISATION.LOG
molecule HMim-Cl (C4H7ClN2)
Calculation Type FREQ
method B3LYP
calculation method RB3LYP
basis set 3-21G
final energy -722.687898
RMS gradient 0.000019
point group C1
Confirmed it is Minima Yes


A-HMim-CL-Molecule Image DM.PNG

Media:A HMIM CL OPTIMISATION.LOG

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me3NH-Cl
Bond Distance: r(N-H)=1.17721Â
Bond Distance: r(N-CH3)=1.47704Â
Bond Distance: r(N-Cl)=2.89156Â


Item Table

         Item               Value     Threshold  Converged?
 Maximum Force            0.000052     0.000450     YES
 RMS     Force            0.000010     0.000300     YES
 Maximum Displacement     0.002398     0.001800     NO 
 RMS     Displacement     0.000450     0.001200     YES

Me3NH-Cl Molecule Optimised Version

Calculation Data

name of submitted log file DM me3NHCL Optimisation.log
molecule Me3NH-Cl
method FOPT
calculation method
basis set 3-21G(d,p)
final energy -632.162045
RMS gradient 0.000394
point group C1
Confirmed it is Minima Yes

Me3NHCl Molecule DM.PNG

Media:DM me3NHCL Optimisation.log

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me3NH-Cl
Bond Distance: r(N-H)=1.16186Â
Bond Distance: r(N-Cl)=2.90049Â
Bond Distance: r(Ch3-H)=1.09119Â

Item Table

 Item               Value     Threshold  Converged?
 Maximum Force            0.000942     0.000015     NO 
 RMS     Force            0.000323     0.000010     NO 
 Maximum Displacement     0.087442     0.000060     NO 
 RMS     Displacement     0.014422     0.000040     NO

Me3NH-Cl Molecule Scanned Version

Calculation Data

name of submitted log file DM me3NHCL RIGID SCAN.log
molecule Me3NH-Cl
method SCAN
calculation method RB3LYP
basis set 3-21G
final energy -632.066188
RMS gradient Blank-No Gradient Listed
point group C1
Confirmed it is Minima Yes

Me3NHCl Molecule Scan DM.PNG

Media:DM me3NHCL RIGID SCAN.log

rotateable 3D Jmol image BH

Bond Distances

Optimised bond distance and angle for Me3NH-Cl
Bond Distance: r(N-H)=0.80000Â
Bond Distance: r(N-Cl)=3.20000Â

Scan of Total Energy

Me3NHCl Molecule Scan of Total Energy DM.PNG

This is the total energy of the scanned molecule. It is a U-Shape. The Raw data is available below for your perusal.

File:Me3NHCl Scan of Total Energy Data.log

Bond Energy Calculations NH3BH3

Calculation Data

E(NH3) -56.557769 AU
E(BH3) -26.615324 AU
E(NH3BH3) -83.224689 AU
ΔE AU) E(NH3BH3)-[E(NH3)+E(BH3)] = -83.224689 - (-56.557769+-26.615324) = -0.051596AU
ΔE Kj/mol) -0.051596AU * 2625.4999 kJ/mol = 1 a.u. = -135.46529284 kJ/mol



NH3BH3 Molecule

calculation data

name of submitted log file NH3BH3_Optimisation_Log_File.log.log
molecule NH3BH3
method B3LYP
calculation method RB3LYP
basis set 6-31G(d,p)
final energy -83.224689
RMS gradient 0.000001
point group C1
Confirmed it is Minima Yes

NH3BH3 Molecule Image.PNG

Media:NH3BH3_Optimisation_Log_File.log.log

rotateable 3D Jmol image BH

Item Table

 Item               Value     Threshold  Converged?
 Maximum Force            0.000002     0.000015     YES
 RMS     Force            0.000001     0.000010     YES
 Maximum Displacement     0.000041     0.000060     YES
 RMS     Displacement     0.000020     0.000040     YES

Important geometric parameters

Optimised bond distance and angle for BH3
Bond Distance: r(N-H)=1.01847Â
Bond Distance: r(B-H)=1.20977Â
Bond Distance: r(B-N)=1.66771Â

Bond Angle (N-H): 107.88°
Bond Angle (B-H): 113.88°

Low frequencies ---   -3.6199   -0.0014   -0.0010   -0.0009    2.3908    4.5604
Low frequencies ---  263.4365  632.9747  638.4332
Mode 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
wavenumber (cm-1) 263.4365 632.9747 638.4332 638.5054 1069.1617 1069.1617 1196.1866 1203.5225 1203.5771 1328.8170 1676.0434 1676.0577 2471.9811 2532.0716 2532.0950 3464.1021 3581.1459 3581.1541
Symmetry A A A A A A A A A A A A A A A A A A
intensity (arbitrary units) 0.0000 14.0108 3.5475 3.5464 40.5051 40.5105 108.9677 3.4694 3.4694 113.6226 27.5645 27.5669 67.2027 231.2478 231.2478 2.5113 27.9556 27.9571

NH3BH3 Molecule Image.PNG NH3BH3 Molecule Charge Analysis DM.PNG NH3BH3 Molecule Charge Analysis Legend DM.PNG


BH3 Molecule

Calculation Data

name of submitted log file BH3 Optimisation DM.log
molecule BH3
method B3LYP
calculation method RB3LYP
basis set 6-31G(d,p)
final energy -26.615324
RMS gradient 0.000002
point group D3H
Confirmed it is Minima Yes

BH3 Molecule Image.PNG

Media:BH3_Optimisation_Log_File.log.log

rotateable 3D Jmol image BH

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

Important geometric parameters

Optimised bond distance and angle for BH3
Bond Distance: r(N-F)=1.19200Â
Bond Angle (N-F): 120°
Low frequencies --- -11.6940 -11.6861 -6.5543 -0.0002 0.0280 0.4289
Low frequencies --- 1162.9745 1213.1390 1213.1392

Mode 1 2 3 4 5 6
wavenumber (cm-1) 1162.9745 1213.1390 1213.1392 2582.5813 2715.7180 2715.7189
Symmetry A2" E' E' A1' E' E'
intensity (arbitrary units) 92.5282 14.0550 14.0544 0.0000 126.3320 126.3260

BH3 Molecule IR Spectrum DM.PNG BH3 Molecule Charge Analysis DM.PNG BH3 Molecule Charge Analysis Legend DM.PNG



NH3 Molecule

calculation data

name of submitted log file NH3 Optimisation DM.log
molecule NH3
method RB3LYP
basis set 6-31G(d,p)
final energy -56.557769
RMS gradient 0.000000
point group C3V

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

NH3 Image1DM.png

Media:BH3_Optimisation_Log_File.log.log

rotateable 3D Jmol image NH


Important geometric parameters

Optimised bond distance and angle for NH3
Bond Distance: r(N-H)=1.01797Â
Bond Angle: 37.12783°

Low frequencies --- -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162
Low frequencies --- 1089.3674 1693.9284 1693.9284

Mode 1 2 3 4 5 6
wavenumber (cm-1) 1089.3674 1693.9284 1693.9284 3461.3788 3589.9285 3589.9285
Symmetry A1 E E A1 E E
intensity (arbitrary units) 145.4277 13.5571 13.5572 1.0593 0.2699 0.2699

NH3 Image2 IRSpectra DM.png NH3 Image3 Charges DM.PNG NH3 Image4 ChargesTable DM.PNG

Charges N-Atom H-Atom H-Atom H-Atom
Charge -1.125 0.375 0.375 0.375

Project Molecule N2F2

calculation data

name of submitted log file N2F2 MOLECULE 1 DM.log
molecule N2F2
method RB3LYP
basis set 6-31G(d,p)
final energy -309.012413
RMS gradient 0.000000
point group C2V

Item Table

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

N2F2 Image1DM.PNG

Media:N2F2 MOLECULE 1 DM.LOG

rotateable 3D Jmol image Nf


Important geometric parameters

Optimised bond distance and angle for NH3
Bond Distance: r(N-F)=1.28000Â
Bond Distance: r(N=N)=1.23200Â
Bond Angle (N-F): 120°

Low frequencies --- 0.0013 0.0015 0.0017 3.2233 4.3533 5.0998
Low frequencies --- 347.8772 561.2472 771.6105

Mode 1 2 3 4 5 6
wavenumber (cm-1) 347.8772 561.2472 771.6105 949.4548 987.2543 1636.6075
Symmetry A1 A2 B2 A1 B2 A1
intensity (arbitrary units) 0.6108 0.0000 74.7044 75.4125 81.1265 20.5391

N2F2 Image2 IRSpectra DM.PNG N2F2 Image3 Charges DM.PNG N2F2 Image4 ChargesTable DM.PNG

Charges N-Atom F-Atom N-Atom F-Atom
Charge 0.191 -0.191 0.191 -0.191


Questions:

the molecule from the log file does not have bonds between the F and N atoms, what is going on here?
It does have bonds, you just need to change the number from 8 to 1 or 2 to see where the animation connects the bond together.


IR analysis

how many vibrations are expected from the 3N-6 rule?

The 3N-6 rule, calculates the number of vibrational modes in the molecule where N=the total number of atoms. As N2F2 has 4 atoms, N=4. So 3*(4)-6 = 6 vibrational modes are present in N2F2.

why are there only 4 peaks in the IR spectrum?
The molecule is symmetrical so although there are 6 vibrational modes, only 4 modes are visible because the symmetry of the molecule cancels dipole so they do not show up in an IR spectrum.


which vibration is the asymmetric N-F stretch?
The vibration at 775 cm-1 is the asymmetric N-F stretch.

what is the nature of the highest energy vibration?
This is the N=N stretch located at 1640 cm-1. The peak is small which is due to the tight N=N bond not moving that much.

MO analysis:

which MOs are core orbital MOs?
The 1S orbitals of both F atoms and the 1s orbitals of both N atoms. MO's 1-4.

provide a picture of MO 9 and beside it draw the LCAO diagram

N2F2 Image5 MO9 DM.PNG IMG 7525.jpg

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