Difference between revisions of "Wolfeka"

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Line 16: Line 16:
 
|point group|| C1
 
|point group|| C1
 
|}
 
|}
 +
 +
*meant to be C3v
  
 
===Item table===
 
===Item table===
Line 38: Line 40:
  
 
===Optimised molecule image===
 
===Optimised molecule image===
−
[[File:KATW BH3 optimagemol.PNG|150px]]
+
[[File:Me3ClNH KATW image.PNG|150px]]
 
<jmol><jmolApplet>
 
<jmol><jmolApplet>
 
<title>3D BH<sub>3</sub> molecule</title>
 
<title>3D BH<sub>3</sub> molecule</title>
 
<color>#ff82a8</color>
 
<color>#ff82a8</color>
 
<size>200</size>
 
<size>200</size>
−
<uploadedFileContents>BH3 OPTIMIZATION KATW.LOG</uploadedFileContents>
+
<uploadedFileContents>KATW ME3NH-CLACTUAL.LOG</uploadedFileContents>
 
</jmolApplet></jmol>  
 
</jmolApplet></jmol>  
  
 
====Key bond distances and angles====
 
====Key bond distances and angles====
 
{| class="wikitable"
 
{| class="wikitable"
−
|r(B-H) bond distance|| 1.19&Acirc;
+
|r(N-C) bond distance|| 1.48&Acirc;
 +
|-
 +
|r(N-H) bond distance|| 0.80&Acirc;
 +
|-
 +
|r(N-Cl) bond distance|| 3.20&Acirc;
 
|-
 
|-
−
| &theta;(H-B-H) bond angle|| 120&deg;
+
|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;
 
|}
 
|}
  
Line 58: Line 70:
  
  
−
===BH<sub>3</sub> IR spectrum===
+
===NH<sub>3</sub>BH<sub>3</sub> frequencies===
−
[[File:KATW BH3 IR.PNG]]
 
−
 
 
−
===BH<sub>3</sub> frequencies===
 
 
<pre>
 
<pre>
−
  Low frequencies --- -11.6940  -11.6861   -6.5543   -0.0006    0.0280   0.4289
+
  Low frequencies ---   -3.0077  -0.5001   -0.0059   -0.0053  -0.0047   6.2314
−
  Low frequencies --- 1162.9745 1213.1390 1213.1392
+
  Low frequencies ---   81.5384  81.6770  183.6441
 
</pre>
 
</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
 
−
|}
 
−
 
  
  
 +
# Scan of Total Energy
 +
# 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
 +
[File: KATW MeNHCl scan graph1.PNG]
  
 
===Relative energies===
 
===Relative energies===

Latest revision as of 05:51, 13 May 2026

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
  • meant to be C3v

Item table

opt 

         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

Freq 

         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 BH molecule

Key bond distances and angles

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


  1. Scan of Total Energy
  2. X-Axis: Scan Coordinate
  3. Y-Axis: Total Energy (Hartree)
  4. 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

[File: KATW MeNHCl scan graph1.PNG]

Relative energies

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


E(NH3)= E(BH3)= 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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