Leeryan
Contents
Lab1 Marking
It's good that you have a working wiki. However, you have reported wrong bond distance and IR intensities, and have missed to include the torsion angle. 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.
BH3 Molecule
Calculation Data
| Name of submitted log file | BH3_OPTIMISATION_RL.LOG |
| Molecule | BH3 |
| Method | RB3LYP |
| Basis Set | 6-31(d,p) |
| Final Energy | -26.615324 |
| RMS Gradient | 0.000002 |
| 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
Jmol Rotatable Molecule
logfile: Media:BH3_OPTIMISATION_RL.LOG
Optimised NH Molecule |
Important Geometric Parameters
Optimised bond distance and angle for NH3
r(N-H)= 1.192Â
θ(H-N-H)= 119.9°
Vibrational Modes
Low frequencies --- -11.6940 -11.6861 -6.5543 0.0007 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 |
IR Spectrum
NH3BH3 Molecule
Calculation Data
| Name of submitted log file | NH3BH3_OPTIMISATION_RL.LOG |
| Molecule | NH3BH3 |
| Method | RB3LYP |
| Basis Set | 6-31(d,p) |
| Final Energy | -83.224689 |
| RMS Gradient | 0.000001 |
| Point Group | C1 |
In the literature, the point group for the molecule is C3v, but the output has a C1 point group. This could be because...
Item Table
Item Value Threshold Converged? Maximum Force 0.000001 0.000015 YES RMS Force 0.000001 0.000010 YES Maximum Displacement 0.000043 0.000060 YES RMS Displacement 0.000019 0.000040 YES
Optimised Molecule Image
Jmol Rotatable Molecule
logfile: Media:NH3BH3_OPTIMISATION_RL.LOG
Optimised NH Molecule |
Important Geometric Parameters
Optimised bond distance and angle for NH3
r(N-H)= 1.018Â
r(B-H)= 1.210Â
r(N-B)= 1.668Â
θ(H-N-H)= 107.9°
θ(H-B-H)= 113.9°
θ(H-N-B)= 111.0°
θ(H-B-N)= 104.6°
Vibrational Modes
Low frequencies --- -5.0462 -2.8839 -0.0009 -0.0008 -0.0006 0.6098 Low frequencies --- 263.3824 632.9842 638.4292
| Mode | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 |
| Wavenumber (cm-1) | 263 | 633 | 638 | 638 | 1069 | 1069 | 1196 | 1204 | 1204 | 1329 | 1676 | 1676 | 2472 | 2532 | 2532 | 3464 | 3581 | 3581 |
| Symmetry | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A | A |
| Intensity | 0 | 14 | 4 | 4 | 41 | 41 | 109 | 3 | 3 | 114 | 28 | 28 | 67 | 231 | 231 | 3 | 28 | 28 |
IR Spectrum
Association Energy
E(NH3)= -56.557769 a.u.
E(BH3)= -26.615324 a.u.
E(NH3BH3)= -83.224689 a.u.
ΔE= -83.224689 - (-56.557769 - 26.615324) = -0.051595 a.u or -130.33150 kJ/mol
Me3NH-Cl
Calculation Data
| Name of submitted log file | ME3NHCL_OPTIMISATION_RL.LOG |
| Molecule | Trimethylamine Chloride |
| Method | RB3LYP |
| Basis Set | 3-21G(d, p) |
| Final Energy | -632.162083 |
| RMS Gradient | 0.000079 |
| Point Group | C1 |
Item Table and Low Frequencies
Item Value Threshold Converged? Maximum Force 0.000357 0.000450 YES RMS Force 0.000054 0.000300 YES Maximum Displacement 0.003416 0.001800 NO RMS Displacement 0.000902 0.001200 YES
Low frequencies --- -3.4097 -0.0033 -0.0024 -0.0014 4.6007 7.7513 Low frequencies --- 55.8433 56.0482 188.9635
The maximum displacement has not converged to the applied threshold, and its value is approximately twice that of the threshold. However, all the low frequencies reported are between the limits of ±10, so the molecule is very near to fully optimized, and this optimization result is able to be used for a scan.
Structural Information
r(H-Cl)= 1.739Â
r(N-H)= 1.165Â
Optimized structure:
PES Analysis
Log file:File:ME3NHCL OPTIMISATION RL SCAN3A.LOG
The PES scan simulates an increasing bond distance r(N-H), stepping 14 times from 0.8Â to 2.1Â. The minimum energy corresponds to the ion pair of Me3NH+ and Cl- at a distance of 1.1 to 1.2Â. As r(N-H) increases from the minimum, the total energy also increases, showing that the neutral pair of Me3NH and HCl is a much less stable state than the ion pair.
1-methyl-imidazolium chloride (Structure A)
Calculation Table
| Name of submitted log file | HMIMCL_STRUCTUREA_OPTIMISATION_RL.LOG |
| Molecule | 1-methyl-imidazolium chloride |
| Method | RB3LYP |
| Basis Set | 3-21G |
| Final Energy | -722.687898 |
| RMS Gradient | 0.000018 |
| Point Group | C1 |
Log file:File:HMIMCL STRUCTUREA OPTIMISATION RL.LOG
Item Table & Low Frequencies
Item Value Threshold Converged? Maximum Force 0.000046 0.000450 YES RMS Force 0.000010 0.000300 YES Maximum Displacement 0.009564 0.001800 NO RMS Displacement 0.001631 0.001200 NO
Low frequencies --- -5.2982 -2.6328 -0.0039 -0.0029 0.0029 2.7560 Low frequencies --- 36.0122 64.3158 80.7655
The displacement values have not converged; the RMS displacement is very close to the threshold, and the maximum displacement is approximately 5 times larger. Given that the low frequencies were all in acceptable range, it was opted to use this optimisation for the PES scan.
Structural Information
Bond distances:
r(H-Cl)= 1.720Â
r(H-N)= 1.178Â
Optimized Molecule:
PES Analysis
1-methyl-imidazolium chloride (Structure B)
Calculation Table
| Name of submitted log file | HMIMCL_STRUCTUREB_OPTIMISATION_RL.LOG |
| Molecule | 1-methyl-imidazolium chloride |
| Method | RB3LYP |
| Basis Set | 3-21G |
| Final Energy | -722.666200 |
| RMS Gradient | 0.000021 |
| Point Group | C1 |
Log file:File:HMIMCL STRUCTUREB OPTIMISATION RL.LOG
Item Table & Low Frequencies
Item Value Threshold Converged? Maximum Force 0.000037 0.000450 YES RMS Force 0.000010 0.000300 YES Maximum Displacement 0.001264 0.001800 YES RMS Displacement 0.000201 0.001200 YES
Low frequencies --- -5.5466 -3.0692 0.0013 0.0026 0.0038 2.1695 Low frequencies --- 45.2073 162.2239 198.8914
Structural Information
Bond distances:
r(Cl-H1(methyl)) = 2.276
r(Cl-H2) = 2.134
rC(H-Cl) = 2.030 rC(H-Cl(close methyl)) = 2.417 rC(H-Cl(far methyl)) = 4.131
1-methyl-imidazolium chloride (Structure C)
Calculation Table
| Name of submitted log file | HMIMCL_STRUCTUREC_OPTIMISATION_RL.LOG |
| Molecule | 1-methyl-imidazolium chloride |
| Method | RB3LYP |
| Basis Set | 3-21G |
| Final Energy | -722.666200 |
| RMS Gradient | 0.000021 |
| Point Group | C1 |
Log file:File:HMIMCL STRUCTUREC OPTIMISATION RL.LOG
Item Table & Low Frequencies
Item Value Threshold Converged? Maximum Force 0.000066 0.000450 YES RMS Force 0.000014 0.000300 YES Maximum Displacement 0.006632 0.001800 NO RMS Displacement 0.001600 0.001200 NO
Low frequencies --- -3.0686 -2.1693 -0.0010 0.0006 0.0029 3.3295 Low frequencies --- 52.4049 102.2473 107.1324
The displacement values have not converged; the RMS displacement is very close to the threshold, and the maximum displacement is approximately 4 times larger. Given that the low frequencies were all in acceptable range, it was opted to use this optimisation for further analysis.
Structural Information
Bond distances:
rC(H-Cl) = 2.030
rC(H-Cl(close methyl)) = 2.417
rC(H-Cl(far methyl)) = 4.131
NH3 Molecule
Calculation Data
| Name of submitted log file | RL_nh3_optf_pop.log |
| Molecule | NH3 |
| Method | RB3LYP |
| Basis Set | 6-31G(d, p) |
| Final Energy | -56.557769 |
| RMS Gradient | 0.000000 |
| Point Group | C1 |
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
Jmol Rotatable Molecule
logfile: Media:RL_nh3_optf_pop.log
Optimised NH Molecule |
Important Geometric Parameters
Optimised bond distance and angle for NH3
r(N-H)= 1.2Â
θ(H-N-H)= 106°
Vibrational Modes
Low frequencies --- -5.6864 -3.6131 -3.6124 -0.0012 0.0045 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 |
IR Spectrum
Atomic Charges
| Atom | Charge (e) |
| N | -1.125 |
| H1 | 0.375 |
| H2 | 0.375 |
| H3 | 0.375 |
Project Molecule: cis-N2F2
Calculation Data
| Name of submitted log file | leeryan_n2f2_optf.log |
| Molecule | N2F2 |
| Method | RB3LYP |
| Basis Set | 6-31G(d, p) |
| Final Energy | -309.012413 |
| RMS Gradient | 0.000000 |
| Point Group | C2v |
logfile: Media:LEERYAN_N2F2_OPTF.LOG
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
The item table shows that value(s) have converged and the optimisation was successful.
Optimised Molecule Image
Jmol Rotatable Molecule
Optimised NF Molecule |
Important Geometric Parameters
Optimised bond distance and angle for N2F2
r(N-N)= 1.2Â
r(N-F)= 1.4Â
θ(N-N-F)= 114°
Vibrational Modes
Low frequencies --- 0.0008 0.0016 0.0019 3.2233 4.3533 5.0998 Low frequencies --- 347.8772 561.2472 771.6105
All low frequencies in the first row are less than 20, which indicates that the optimisation was successful.
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| Wavenumber (cm-1) | 348 | 561 | 772 | 949 | 987 | 1637 |
| Symmetry | A1 | A2 | B2 | A1 | B2 | A1 |
| Intensity | 0 | 15 | 75 | 75 | 81 | 21 |
IR Spectrum
Atomic Charges
| Atom | Charge (e) |
| N1 | 0.215 |
| N2 | 0.215 |
| F1 | -0.215 |
| F2 | -0.215 |
Questions about N2F2
1. Why does the visualisation from the .log file not show N-F bonds?
This is likely an 'error' imposed from the Gaussian program, as the distance between of 1.4Â is a reasonable bond length. During optimisation, whether the bond actually exists is not necessarily considered, so longer bonds within the molecule might not be visualized correctly when viewing the .log file.
2. How many vibrations are expected from the 3N - 6 rule?
There are four atoms (2 N and 2 F), so: (3 × 4) - 6 = 12 - 6 = 6. There are six vibrations expected.
3. Why are only 4 peaks visible in the IR spectrum?
cis-N2F2 is highly symmetrical, so some specific vibrational modes do not have an overall dipole moment. The vibrational modes calculated at 348 cm<sup)-1 and 561 cm-1 have low intensity on an IR because of their low overall dipole moment.
4. Which vibration is the asymmetric N-F stretch?
The vibration at 949 cm-1 is the asymmetric N-F stretch.
5. What is the nature of the highest energy vibration?
The highest energy vibration at 1637 cm-1 is the N=N stretch.
6. Which molecular orbitals are core MOs?
The core molecular orbitals are MOs 1, 2, 3 and 4.
7. Provide a picture of MO9 and draw an LCAO diagram.
Molecular orbital 9:
LCAO diagram:
