Difference between revisions of "Caseycame"
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==Lab1 Marking== | ==Lab1 Marking== | ||
| − | Your reported intensities of vibrational data | + | Your reported intensities of vibrational data are incorrect for NH3 molecule. Also, the geometric parameters for N2F2 are incomplete. Overall a decent attempt. If you have any specific questions, do email Prof. Hunt. |
==NH<sub>3</sub> Ammonia Molecule== | ==NH<sub>3</sub> Ammonia Molecule== | ||
Revision as of 01:41, 7 May 2026
Contents
Lab1 Marking
Your reported intensities of vibrational data are incorrect for NH3 molecule. Also, the geometric parameters for N2F2 are incomplete. Overall a decent attempt. If you have any specific questions, do email Prof. Hunt.
NH3 Ammonia Molecule
Log file: File:CJC2026 NH3DUPE OPTF.LOG
Calculation data
| Name of submitted log file | cjc2026_nh3_optf.log |
| Molecule | NH3 |
| Calculation method | RB3LYP |
| Basis set reported | 6-31G(d,p) |
| Final reported energy | -56.557769 au |
| RMS gradient | 0.00000 au |
| Point group of NH3 | C3v |
Item Table
Low frequencies: -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162
Low frequencies: 1089.3674 1693.9284 1693.9284
Optimised molecule image
Interactive 3D molecule |
Important geometric parameters
Optimised bond distance and angle for NH3
r(N-H)=1.02Â
θ(H-N-H)=106°
Vibration as wavenumbers
| Vibration | Wavenumber (cm-1) | Infrared (arbitrary units) |
| 1 | 1089 | 145 |
| 2 | 1694 | 13 |
| 3 | 1694 | 14 |
| 4 | 3461 | 1 |
| 5 | 3590 | 1 |
| 6 | 3590 | 1 |
Vibrations and Symmetries
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| wavenumber (cm-1) | 1089 | 1694 | 1694 | 3461 | 3590 | 3590 |
| Symmetry | A1 | E | E | A1 | E | E |
| IR Intensity (arbitrary units) | 145 | 14 | 14 | 1 | 1 | 1 |
Charge Distribution
The nitrogen atom has a relevant charge of -1.125, and the hydrogen atoms have relevant charges of 0.375
N2F2 cis-dinitrogen difluoride molecule
Log file: File:Cjc2026 n2f2 optf.log
Calculation Data
| Name of submitted log file | cjc2026_n2f2_optf.log |
| Molecule | N2F2 |
| Calculation method | RB3LYP |
| Basis set reported | 6-31G(d,p) |
| Final reported energy | -309.01241 au |
| RMS gradient | 0.00000 au |
| Point group of N2F2 | C2v |
Item Table
Low frequencies: 0.0013 0.0014 0.0017 2.5281 4.1168 4.5862
Low frequencies: 343.8551 569.1750 768.8358
Optimised molecule image
Interactive 3D molecule |
Important geometric parameters
Optimised bond distance and angle for N2F2
r(N-f)=1.39Â
θ(F-N-N-F)=0°
Vibrations as wavenumbers
| Vibration | Wavenumber (cm-1) | Infrared (arbitrary units) |
| 1 | 348 | 1 |
| 2 | 561 | 0 |
| 3 | 772 | 75 |
| 4 | 949 | 75 |
| 5 | 987 | 81 |
| 6 | 1637 | 21 |
Vibrations and Symmetries
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| wavenumber (cm-1) | 348 | 561 | 772 | 949 | 987 | 1637 |
| Symmetry | A1 | A2 | B2 | A1 | B2 | A1 |
| IR Intensity (arbitrary units) | 1 | 0 | 75 | 75 | 81 | 21 |
Charge Distribution
The nitrogen atoms have relative charges of 0.125 and the fluorine atoms have relative charges of -0.125
IR spectrum discussion
One would expect cis-N2F2 to have 6 vibrations from the 3N-6 rule, as it is a non-linear molecule. It has 4 atoms (N), so 3*(4)-6 = 6.
Four IR peaks can be seen despite 6 vibrations because the 1st and 2nd vibrations have an IR value of 0, so are functionally not detected in an IR spectrum. It is only vibrations 3-6, with detectable IR values, which show up on the graph pictured above.
The asymmetric N-F stretch is vibration 3.
The nature of the highest energy vibration is the one with the highest frequency, or vibration 6. Its nature, in the sense of movement, is the symmetric stretching of the N=N bond.
Molecular Orbital Analysis
The core molecular orbitals for cis-N2F2 are the first 4 molecular orbital, as they correspond to the molecular orbitals that are not involved in bonding.
The image above is molecular orbital 9 and besides it is it's drawn LCAO diagram.
BH3 Borane Molecule
Log file: File:CJC BH3 OPTFREQ.LOG
Calculation data
| Name of submitted log file | CJC_BH3_optfreq.log |
| Molecule | BH3 |
| Calculation method | RB3LYP |
| Basis set reported | 6-31G(d,p) |
| Final reported energy | -26.615324 au |
| RMS gradient | 0.000004 au |
| Point group of BH3 | D3h |
Item Table
Low frequencies: -2.3197 -0.8408 -0.0192 0.0005 2.1620 9.6378
Low frequencies: 1163.0180 1213.1682 1213.1684
The fact that all parameters have successfully converged and the gradient is less than 0.0005 is indicative that the optimisation ran without issue, and that this BH3 is indeed a minima.
Optimised molecule image
Interactive 3D molecule |
Important geometric parameters
Optimised bond distance and angle for BH3
r(B-H)=1.19Â
θ(H-B-H)=120°
NH3BH3 Aminoborane Molecule
Log file: File:CJC NH3BH3 OPTFREQ.LOG
Calculation data
| Name of submitted log file | CJC_NH3BH3_optfreq.log |
| Molecule | NH3BH3 |
| Calculation method | RB3LYP |
| Basis set reported | 6-31G(d,p) |
| Final reported energy | -83.224689 au |
| RMS gradient | 0.000002 au |
| Point group of NH3BH3 | C3v |
Item Table
Low frequencies: -7.3279 -1.3977 -1.3955 -0.0012 0.0387 0.2910
Low frequencies: 263.2450 632.9557 638.4412
The fact that all parameters have successfully converged and the gradient is less than 0.0005 is indicative that the optimisation ran without issue, and that this NH3BH3 is indeed a minima.
Optimised molecule image
Interactive 3D molecule |
Important geometric parameters
Optimised bond distance and angle for NH3BH3
r(N-H)=1.02Â
r(B-H)=1.21Â
r(N-B)=1.67Â
θ(H-N-H)=108°
θ(H-B-H)=114°
Energies
Energy of NH3 = -56.557769 au
Energy of BH3 = -26.615324 au
Energy of NH3BH3 = -83.224689 au
Association energy may be measured as a change of energy (ΔE) of the product molecule from the reactant fragments
ΔE = E(NH3BH3)-[E(NH3)+E(BH3)]
ΔE = -83.224689- [-56.557769 + -26.615324]
ΔE = -0.051596 au = -135kJ/mol
IL ion-pair Me3NH-Cl
Log file: File:CJC ME3NH-CL OPTFREQ.LOG
Last (freq) Item Table
Second-last (opt) Item Table
Low frequencies: -8.3392, -0.0023, 0.0022, 0.0022, 3.1203, 5.2719
Low frequencies: 55.1484, 56.4401, 190.1223
The low frequencies are between -10 and +10 and the forces have converged successfully during the optimisation, which is to be expected.
Important geometric parameters
Optimised bond distance and angle for Me3NH-Cl
r(N-H)=1.16Â
r(N-Cl)=2.90Â
After this optimisation the N-H bond distance was set to 0.8Â and the N-Cl bond distance was set to 3.2Â.
Optimised molecule image
Interactive 3D molecule |
Scanned molecule image
Interactive 3D molecule |
The scanned Me3NH-Cl molecule has a energy minimum at transition mode 5, as shown above, which corresponds to a r(N-H) of 1.2Â and an energy of -632.1538028au, as can be seen in the below data and graph.
HMim-Cl Molecule A
Log file: File:CJC HMIM-CL OPTFREQA.LOG
Calculation data
| Name of submitted log file | CJC_HMim-Cl_optfreqA.log |
| Molecule | 1-methyl-imidazolium chloride |
| Calculation method | RB3LYP |
| Basis set reported | 3-21G |
| Final reported energy | -722.6879 au |
| RMS gradient | 0.00000 au |
| Point group of HMim-Cl | C1 |
Item Table
Low frequencies: -5.1216 -2.7800 -0.0031 -0.0010 0.0003 2.7779
Low frequencies: 36.1409 64.4125 80.7954
Bond Distances of A
r(N-H): 1.18Â
r(C-H): 1.07Â
Rigid scan of A
Log file: File:CJC HMIM-CL RIGIDSCANA.LOG
Image of the raw PES graph
The two protonation states for HMim-Cl
HMim-Cl as an ionic liquid pair is of lower association energy than MeNH-Cl, meaning HMim-Cl is a more energetically favourable ionic liquid species. The N-H bond distance that is most favourable for MeNH-Cl is the fifth transition mode, being 1.2Â, whilst for HMim-Cl it is the fourth transition mode, being 1.1Â. Upon analysing the numbers, one may notice that the energies of MeNH-Cl gently trend upwards as distance increase after 1.2Â, whilst for HMim-Cl the energies increase uniformly for 6 modes, then start decreasing again. This suggests that MeNH-Cl has a clear energy medium at 1.2Â whereas HMim-Cl has another local minima when the hydrogen atom is much nearer the chloride anion than the main ring body. This is a sensible result given that HMim-Cl has two protonation modes, perhaps each with their own minimal energies with distance.
HMim-Cl Molecule B
Log file: File:CJC HMIM-CL OPTFREQB.LOG
Calculation data
| Name of submitted log file | CJC_HMim-Cl_optfreqB.log |
| Molecule | 1-methyl-imidazolium chloride |
| Calculation method | RB3LYP |
| Basis set reported | 3-21G |
| Final reported energy | -722.666201 au |
| RMS gradient | 0.00000 au |
| Point group of HMim-Cl | C1 |
Item Table
Low frequencies: -5.0505 -2.6130 -0.0038 -0.0027 0.0017 1.5094
Low frequencies: 45.4482 162.0658 198.7872
Bond Distances of B
r(N-H): 1.01Â
r(C-H): 1.10Â
HMim-Cl Molecule C
Log file: File:CJC HMIM-CL OPTFREQC ACTUAL1.LOG
Calculation data
| Name of submitted log file | CJC_HMim-Cl_optfreqC_ACTUAL1.log |
| Molecule | 1-methyl-imidazolium chloride |
| Calculation method | RB3LYP |
| Basis set reported | 3-21G |
| Final reported energy | -761.777250 au |
| RMS gradient | 0.00000 au |
| Point group of HMim-Cl | C1 |
Item Table
Log file: 
Low frequencies: -4.4515 -0.0022 -0.0019 -0.0018 4.5466
Low frequencies: 91.4317 110.8817 147.7972
Bond Distances
No N-H bonds to report.
r(C-H): 1.07Â
A, B, and C comparison
Energies
Energy of HMim-Cl A = -722.687900 au = -1897417 kJ/mol
Energy of HMim-Cl B = -722.666201 au = -1897360 kJ/mol
Energy of HMim-Cl C = -761.777250 au = -2000046 kJ/mol
The relative energy of isomers may be calculated by subtracting the energy of the most stable isomer from the others, in this case the isomers in question are A and B. A is the more stable isomer, as it has a lower energy, so its energy will be subtracted from B.
Relative energy = E(B) - E(A) = -1897360 kJ/mol - -1897417 kJ/mol = 57 kJ/mol
The reason molecule B is a less stable conformer may be due to the molecule's interaction with the chloride anion being shared between two functional groups, being the methyl and methine carbons. However, despite the interaction being shared between two different functional groups, the chloride is interacting with two carbon groups that already have a favoured number of substituents, so the chloride's interaction is creating strain in each carbon group, thereby increasing the association energy for molecule B. This may be contrasted with molecule A, where the chloride anion is interacting with a hydrogen. While the hydrogen also is bound to a favourable number of substituents, hydrogen is less large a molecule and less electronegative than carbon, and therefore the chloride's interaction creates less a strain and the association energy is less.
Dissociation energy may be measured as the inverse energy to the association energy of the species. In this case, it is assumed that the energies listed above are the association energies for each isomer, so the dissociation energies must be proportionately inverse to the energies needed to form the isomers and their involved bonds. For instance, molecule C has the lowest value for the association energies of each isomer, therefore its bonds must be easiest to form but must require more energy to break. Molecule C has two methyl substituents bound to the central ring as opposed to isomers A and B, which have only one. The chloride is interacting with a carbon atom, which itself is flanked by two other carbons which are bound to one each of the methyl groups. This means that the carbon which the chloride is interacting with is more stabilised, as the charge discrepancy the interaction creates can become delocalised to more carbon centres, thereby making this interaction and isomer a more favourable conformation than A and B. A and B have less ways to delocalise a change in charge which makes their association less favourable, but their dissociation more favourable.
