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== NH<sub>3</sub> Molecule == | == NH<sub>3</sub> Molecule == | ||
Revision as of 06:06, 8 May 2025
Contents
- 1 Comments
- 2 NH3 Molecule
- 3 N2F2 Project Molecule
- 4 Computational lab 2
- 4.1 Association energies: Ammonia-Borane
- 4.2 Assessment of association energy
- 4.3 Ionic Liquid Ion-Pair Me3NH-Cl
- 4.4 Ionic Liquid Ion-Pairs
- 4.5 Assessment of Hydrogen Bonding for HMim-Cl, MMim-Cl and Me3NH-Cl
- 4.6 Optimising individual ions
- 4.7 Association energy of imidazolium ion pairs
- 4.8 Scan of HMim-Cl(a)
Comments
You've done a great job overall well done! However, it would have been nice if you had focused a bit more on enhancing the visual appeal of the wiki. If you have any query, please contact Prof. Hunt.
NH3 Molecule
NH3 log file: Media: VDL_NH3_OPTF_POP.LOG
Calculation data
| Name of submitted log file | VDL_NH3_OPTF_POP.LOG |
| Molecule | NH3 |
| Method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy | -56.557769 |
| RMS gradient | 0.000000 |
| Point group | C3V |
Where energy was measured in Hartrees and RMS gradient in Hartree/Bohr.
Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
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
The low frequencies are checked to ensure the geometry of NH3 have fully converged.
Low frequencies --- -5.6864 -3.6131 -3.6124 0.0017 0.0048 0.0162 Low frequencies --- 1089.3674 1693.9284 1693.9284
Since none of the low frequencies in the first line have surpassed ±20cm-1, the geometry is fully converged.
Optimised NH3 molecule
logfile:Media: VDL_NH3_OPTF_POP.LOG
Jmol rotatable NH3 molecule
Optimised molecule |
Important geometric parameters
Optimised bond distance and angle for NH3
| coord | value |
| r(N-H) | 1.02Â |
| θ (H-N-H) | 106° |
Vibrations
Table of vibrations:
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| Wavenumber (cm-1) | 1089 | 1694 | 1694 | 3461 | 3590 | 3590 |
| Symmetry | A1 | E | E | A1 | E | E |
| Intensity (arbitary units) | 145 | 14 | 14 | 1 | 0 | 0 |
NH3 Infrared Spectrum
Questions about the infra-red spectrum:
How many modes do you expect from the 3N-6 rule?
- Since there are four atoms in NH3, N=4. We expect to have six modes.
How many bands (peaks) do you see in the computed spectrum of gaseous ammonia?
- There are two peaks in the spectrum, although we calculated all six of them.
Which modes are degenerate (ie have the same energy)?
- At both 1694 (modes 2 and 3) and 1590cm-1 (modes 5 and 6) there are two degenerate modes.
Which modes have essentially no intensity?
- The 3461 cm-1 and 3590cm-1 modes (4,5 and 6) have very low intensity.
Why are there fewer modes in the spectrum than you would predict from the 3N-6 rule?
- Due to some of the modes having no intensity and some others being degenerate which are included in the same peak.
Which modes are "bending" vibrations and which are "bond stretch" vibrations?
- The stretching modes are of higher energy, which are modes 4, 5 and 6. The bending modes are of lower energy, modes 1, 2 and 3.
One mode is known as the "umbrella" mode, which one is this?
- This is the first mode based on the animation, showing the hydrogen atoms oscillating up and down like how an umbrella would open.
Why is the umbrella mode so intense?
- Mode 1 is really intense because it has a large dipole moment change due to the oscillating vibrations it undergoes.
Charges
The image of the NBO charges are coloured red for negative and green for positive. The range is between -1.125 to +1.125e.
Table of NH3 charges
| Atom | Charge |
|---|---|
| N | -1.13 |
| H | +0.38 |
Molecular Orbitals
| the real 2a1 MO | the LCAO MO |
|---|---|
 |
|
N2F2 Project Molecule
Computing the cis isomer.
N2F2 log file: Media: VDL_N2F2_OPTF_POP.LOG
Calculation data
| Name of submitted log file | VDL_N2F2_OPTF_POP.LOG |
| Molecule | N2F2 |
| Method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy | -309.01241 |
| RMS gradient | 0.000000 |
| Point group | C2V |
Where energy was measured in Hartrees and RMS gradient in Hartree/Bohr.
Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
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 low frequencies are checked to ensure the geometry of NH3 have fully converged.
Low frequencies --- 0.0007 0.0013 0.0019 3.2233 4.3533 5.0998 Low frequencies --- 347.8772 561.2472 771.6105
Since none of the low frequencies in the first line have surpassed ±20cm-1, the geometry is fully converged.
Optimised N2F2 molecule image
logfile:Media: VDL_N2F2_OPTF_POP.LOG
Where are the bonds for the optimised N2F2?
The optimised N2F2 didn't have any bonds when it was opened as a log file likely due to the optimisation exceeding the distance criteria in Gaussview.
Although visually there are missing bonds from the nitrogen to fluorine, they do exist as seen in the checkpoint file.
Jmol rotatable N2F2 molecule
Optimised molecule |
Important geometric parameters
Optimised bond distances and angle for N2F2
| coord | value |
| r(F-N) | 1.39Â |
| r(N=N) | 1.22Â |
| θ (F-N=N) | 114° |
Vibrations
Table of vibrations:
| Mode | 1 | 2 | 3 | 4 | 5 | 6 |
| Wavenumber (cm-1) | 348 | 561 | 772 | 949 | 987 | 1637 |
| Symmetry | A1 | A2 | B2 | A1 | B2 | A1 |
| Intensity (arbitary units) | 1 | 0 | 75 | 75 | 81 | 21 |
N2F2 Infrared Spectrum
IR analysis
How many vibrations are expected from the 3N-6 rule?
- Since there are four atoms in N2F2, N=4. We expect to have six modes.
Why are there only 4 peaks in the IR spectrum?
- The IR spectrum only displays 4 peaks due to the intensities of the modes. Mode 1 is positioned at 348cm-1 with an intensity of 1 (with arbitrary units) and is not visible on the IR spectrum. Similarly for mode 2 at 562cm-1 it has an intensity of 0 (with arbitrary units) and is therefore not visible. This is because they both have no dipole moment change. This results in modes 3-6 (4 peaks) being show in the infrared spectrum.
Which vibration is the asymmetric N-F stretch?
- Mode 3 which is at 772cm-1 with an intensity of 75 (arbitrary units) is the asymmetric N-F stretch. This was determined after visualising the vibrations of mode 1.
What is the nature of the highest energy vibration?
- The highest energy vibration is at 1637cm-1 and is the N-N stretch where the nitrogen atoms are moving a part from each other in a symmetric fashion.
Charges
The image of the NBO charges are coloured red for negative and green for positive. The range is between -1.125 to +1.125e, the same as molecule NH3.
Table of N2F2 charges:
| Atom | Charge |
|---|---|
| N | 0.22 |
| F | -0.22 |
NH3 and N2F2 can be compared because they are set to the same type of charge distribution and scale. Since the charges are less for N2F2, it has much less of a dipole moment which makes sense due to the similarities in electronegativity for nitrogen and fluorine compared to nitrogen and hydrogen.
Molecular Orbitals
| MO9 | the LCAO MO |
|---|---|
 |
|
Molecular Orbital analysis
The core molecular orbitals for N2F2 are the molecular orbitals 1-4 visualised in Gaussview. Molecular orbital 1 is the in-phase 1s orbitals of fluorine, whilst molecular orbital 2 is the out of phase 1s orbitals of fluorine. Molecular orbital 3 are the 1s orbitals of nitrogen in-phase, whilst molecular orbital 4 is the 1s orbitals of the nitrogens out of phase.
Computational lab 2
Association energies: Ammonia-Borane
The reactants NH3 and BH3 and product NH3BH3. Each molecule will be undergo optimisation and frequency analysis to assess association energy
BH3
BH3 log file: Media: VDL_BH3_OPTIMISATION.LOG
Calculation data
| Name of submitted log file | VDL_BH3_OPTIMISATION.LOG |
| Molecule | BH3 |
| Method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy | -26.615324 |
| RMS gradient | 0.000002 |
| Point group | D3H |
BH3 Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
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
The low frequencies are checked to ensure the geometry of BH3 have fully converged.
Low frequencies --- -11.6940 -11.6861 -6.5543 -0.0005 0.0280 0.4289 Low frequencies --- 1162.9745 1213.1390 1213.1392
Since none of the low frequencies in the first line have surpassed ±20cm-1, the geometry is fully converged.
Jmol rotatable BH3 molecule
Optimised molecule |
NH3BH3
NH3BH3 log file: Media: VDL_NH3BH3_OPTF.LOG
Calculation data
| Name of submitted log file | VDL_NH3BH3_OPTF.LOG |
| Molecule | NH3BH3 |
| Method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy | -83.224689 |
| RMS gradient | 0.000003 |
| Point group | C3V |
NH3BH3 Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
Item Value Threshold Converged?
Maximum Force 0.000005 0.000015 YES
RMS Force 0.000002 0.000010 YES
Maximum Displacement 0.000047 0.000060 YES
RMS Displacement 0.000022 0.000040 YES
The low frequencies are checked to ensure the geometry of NH3BH3 have fully converged.
Low frequencies --- -6.3823 -2.4027 -2.3898 0.0004 0.0226 0.1764 Low frequencies --- 263.2889 632.9912 638.4485
Since none of the low frequencies in the first line have surpassed ±20cm-1, the geometry is fully converged.
Jmol rotatable NH3BH3 molecule
Optimised molecule |
Assessment of association energy
Energies for reactants and product in atomic units
| NH3 | -56.557769 |
| BH3 | -26.615324 |
| NH3BH3 | -83.224689 |
Calculating the association energy:
ΔE = E(NH3BH3)-[E(NH3)+E(BH3)]
ΔE = -0.051597Au
ΔE = -135KJmol-1
The energy required for the reactants NH3 and BH3 to form NH3BH3 is -135KJmol-1.
Ionic Liquid Ion-Pair Me3NH-Cl
The ionic liquid (IL) ion-pair Me3NH-Cl was first optimised. A rigid scan of the optimised structure was then taken to move the hydrogen along the N and Cl coordinate path to analyse its "potential energy surface".
Optimisation of Me3NH-Cl
Two log files have been displayed to demonstrate that the first optimisation had trouble converging. Upon analysis of the optimisation viewed in GaussView, a flat potential energy surface was observed where after about 20 scans the energy remained at the minima. A frequency analysis was complete on the last optimised structure to observe the low frequencies which were within the ±10cm-1 range. This suggested that the optimisation was successful and that we could now carry out the scan.
This is the first optimised log file:
Me3NH-Cl log file:
Media: VDL_ION_PAIR_ME3NH-CL_OPTF.LOG
Me3NH-Cl log file:
Media: VDL_ION_PAIR_ME3NH-CL_FREQ.LOG
From the first file with optimisation and frequency
Item Value Threshold Converged?
Maximum Force 0.000158 0.000015 NO
RMS Force 0.000033 0.000010 NO
Maximum Displacement 0.008698 0.000060 NO
RMS Displacement 0.002748 0.000040 NO
From the frequency file to check
Item Value Threshold Converged?
Maximum Force 0.000073 0.000450 YES
RMS Force 0.000023 0.000300 YES
Maximum Displacement 0.004700 0.001800 NO
RMS Displacement 0.001594 0.001200 NO
From the job where both optimisation and freuquency was run, the last item table indicates that the forces and displacements both haven't converged. However, the frequency job run on the last optimised structure has both forces converged but not the displacement. This is due to the flat potential energy surface and poor basis-sets (since we have used the 3-21G to save time).
Low frequencies --- -7.3344 -3.3531 -0.0041 -0.0040 -0.0002 4.9738 Low frequencies --- 55.8338 56.2362 190.1004
Low frequencies were within the ±10cm-1 range
Optimised bond distances and angle for Me3NH-Cl
| coord | value |
| r(N-H) | 1.164Â |
| r(N-Cl) | 2.902Â |
Rigid scan of the optimised Me3NH-Cl
Me3NH-Cl log file:
Media:VDL_ION_PAIR_ME3NH-CL_RIGID_SCAN.LOG
The raw data directly from Gaussview is copied below:
X Y 0.800000000 -632.073827478 0.900000000 -632.129658775 1.000000000 -632.153314083 1.100000000 -632.161137302 1.200000000 -632.161862214 1.300000000 -632.159678039 1.400000000 -632.156136268 1.500000000 -632.151083781 1.600000000 -632.142662788 1.700000000 -632.126547543 1.800000000 -632.094608135 1.900000000 -632.032875764
A plot of the rigid scan of the optimised Me3NH-Cl:
About the plot: The plot was created in excel by manipulating the raw energy data to data relative to the lowest energy N-H position. This plot depicts the bonding interaction between the two ions and how the potential energy changes as the N-H bond distance varies in 0.1Å along the N-Cl coordinate path. This ion pair exists as a stable pair when the hydrogen is bonded to the NMe3 forming Me3NH+ and Cl-. This means that the neutral species, without proton transfer is unstable. Additionally there is also a doubly ionic hydrogen-bond between the ions Me3NH+ and Cl- which means that the single hydrogen is able to participate in two hydrogen bonds.
Ionic Liquid Ion-Pairs
Two HMim-Cl and one MMim-Cl ion pair will be optimised.
(a) HMim-Cl
This ion pair is HMim-Cl where the Cl is attracted to the H attached to the nitrogen in the imidazolium ring.
HMim-Cl (a) log file: Media: VDL_A_HMIMCL_IONPAIR_OPT.LOG
HMim-Cl (a) frequency file: Media: VDL_A_HMIMCL_IONPAIR_F.LOG
Calculation data
| Name of submitted log file | VDL_A_HMIMCL_IONPAIR_OPT.LOG |
| Molecule (a) | HMim-Cl |
| Method | RB3LYP |
| Basis set | 3-21G |
| Final energy | -722.687898 |
| RMS gradient | 0.000005 |
| Point group | C1 |
HMim-Cl (a) Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
Item Value Threshold Converged?
Maximum Force 0.000011 0.000450 YES
RMS Force 0.000003 0.000300 YES
Maximum Displacement 0.001056 0.001800 YES
RMS Displacement 0.000210 0.001200 YES
Low frequencies --- -4.7565 -2.6851 -0.0026 -0.0011 -0.0001 3.0008 Low frequencies --- 36.1454 64.5456 80.9235
(b) HMim-Cl
HMim-Cl (b) log file: Media: VDL_B_HMIMCL_IONPAIR_OPT.LOG
HMim-Cl (b) frequency file:Media: VDL_B_HMIMCL_IONPAIR_F.LOG
Calculation data
| Name of submitted log file | VDL_B_HMIMCL_IONPAIR_OPT.LOG |
| Molecule (b) | HMim-Cl |
| Method | RB3LYP |
| Basis set | 3-21G |
| Final energy | -722.666200 |
| RMS gradient | 0.000010 |
| Point group | C1 |
HMim-Cl (b) Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
Item Value Threshold Converged?
Maximum Force 0.000021 0.000450 YES
RMS Force 0.000005 0.000300 YES
Maximum Displacement 0.000934 0.001800 YES
RMS Displacement 0.000238 0.001200 YES
Low frequencies --- -5.0055 -2.7883 -0.8008 -0.0012 0.0027 0.0028 Low frequencies --- 45.3740 161.9932 198.8467
(c) MMim-Cl
MMim-Cl (c) log file: Media: VDL_C_MMIMCL_IONPAIR_OPT.LOG
MMim-Cl (c) frequency file: Media: VDL_C_MMIMCL_IONPAIR_F.LOG
Calculation data
| Name of submitted log file | VDL_C_MMIMCL_IONPAIR_OPT.LOG |
| Molecule (c) | MMim-Cl |
| Method | RB3LYP |
| Basis set | 3-21G |
| Final energy | -761.779525 |
| RMS gradient | 0.000006 |
| Point group | C1 |
MMim-Cl (c) Convergence
The item table demonstrates that the forces and displacements have converged successfully as none of them exceed their respective thresholds.
Item Value Threshold Converged? Maximum Force 0.000015 0.000450 YES RMS Force 0.000004 0.000300 YES Maximum Displacement 0.000543 0.001800 YES RMS Displacement 0.000127 0.001200 YES
Low frequencies --- -3.5666 -3.0667 -0.0021 -0.0007 0.0025 2.1253 Low frequencies --- 52.1666 102.5222 107.1217
Assessment of Hydrogen Bonding for HMim-Cl, MMim-Cl and Me3NH-Cl
Table comparing the H---Cl distance for all ion-pairs:
| coord | HMim-Cl (a) | HMim-Cl (b) | MMim-Cl(c) | Me3NH-Cl |
| r(H-Cl) | 1.719Â | - | - | 1.738Â |
| r(CH3 - Cl) | - | 2.278Â | - | - |
| r(CH-Cl) | - | 2.134Â | 2.030Â | - |
Description of hydrogen bonding
The hydrogen bond (H---Cl) of HMim-Cl (a) is shorter than the hydrogen bond in Me3NH-Cl by 0.019Â. This indicates that the hydrogen bond for HMim-Cl is stronger than Me3NH-Cl due to larger electrostatic forces of attraction.
Both HMim-Cl (a) and Me3NH-Cl have hydrogen bonds (H---Cl) connected to a nitrogen, whereas HMim-Cl (b) and MMim-Cl (c) have the hydrogen connected to a carbon. The hydrogen bonds of the N-H bonds are much stronger than the hydrogen bonds of C-H. This due to the differences in bond length, with both hydrogen bonds connected to nitrogen being 1.719Â and 1.738Â in length compared to the bond lengths of 2.278Â, 2.134Â and 2.030Â. The difference in bonds lengths could be related to electronegativity where carbon is less electronegative than nitrogen.
The Van der Waals for hydrogen and chlorine is 120pm and 175pm respectively, which results in a 295pm or 2.95Â bond length when added together. The hydrogen bonds of all the ion-pairs are shorter than this, suggesting they are very strong bonds which are indicative of hydrogen bonding. Hmim-Cl (a) is the strongest hydrogen bond, differing from the Van der Waals distance by 1.231Â.
The ionic nature of the HMim-Cl, MMim-Cl and Me3NH-Cl ion-pairs have an effect on the distance assessment of hydrogen-bonding due to the strong electrostatic attractions between the cations and anions which shorten the bond length.
Optimising individual ions
Optimisation of the HMim+ cation for the HMim-Cl ion pairs
HMim+ log file: Media: VDL_HMIM_CATION_OPTF.LOG
HMim+ Convergence
Item Value Threshold Converged? Maximum Force 0.000010 0.000450 YES RMS Force 0.000002 0.000300 YES Maximum Displacement 0.000655 0.001800 YES RMS Displacement 0.000164 0.001200 YES
Low frequencies --- -0.0010 -0.0005 -0.0003 1.3000 3.5028 4.6209 Low frequencies --- 80.9268 248.1644 352.9285
MMim+ Convergence
Optimisation of the MMim+ cation for the MMim-Cl ion pairs
MMim+ log file: Media: VDL_MMIM_CATION_OPTF.LOG
The last item table in the log file:
Item Value Threshold Converged?
Maximum Force 0.000012 0.000450 YES
RMS Force 0.000004 0.000300 YES
Maximum Displacement 0.013111 0.001800 NO
RMS Displacement 0.005083 0.001200 NO
The second to last item table from the log file:
Item Value Threshold Converged? Maximum Force 0.000012 0.000450 YES RMS Force 0.000004 0.000300 YES Maximum Displacement 0.001579 0.001800 YES RMS Displacement 0.000610 0.001200 YES
The low frequencies:
Low frequencies --- 0.0000 0.0005 0.0006 1.3076 2.4615 3.7650 Low frequencies --- 71.4791 73.4577 193.2873
When analysing the log file for the optimisation and frequency job, the last item table displayed converged forces and not converged displacements. The RMS displacement was close to the threshold, whereas the maximum displacement was quite a lot larger than the threshold. The previous item table (second to last) was analysed to check for convergence. Both forces and displacements had converged successfully and with further check of the low frequencies these were well in the ±10cm-1 range. Therefore the MMim+ has optimized successfully.
Cl- Convergence
Optimisation of the Cl- anion for the MMim-Cl ion pairs
Cl- log file: Media: VDL_CL_ANION_ENERGY.LOG
Association energy of imidazolium ion pairs
Table of individual energies for ions and ion-pairs:
| Ion or ion-pair | energy (Au) |
| HMim+ cation | -264.455119 |
| MMim+ cation | -303.559223 |
| Cl- anion | -458.057087 |
| HMim-Cl (a) ion pair | -722.687897 |
| HMim-Cl (b) ion pair | -722.666200 |
| MMim-Cl (c) ion pair | -761.779525 |
Table of association energies:
| Ion or ion-pair | energy (Au) | energy (kJmol-1) |
| HMim-Cl (a) | -0.175692 | -461 |
| HMim-Cl (b) | -0.153995 | -404 |
| MMim-Cl (c) | -0.163215 | -429 |
The relative energy between HMim-Cl isomers (a and b):
ΔE = -404kJmol-1 - (-461kJmol-1) = 57kJmol-1
The HMim-Cl (a) isomer is more stable than isomer (b). This is because it is lower in energy by 57kJmol-1 and (a) isomer has a stronger hydrogen bonding due to its much shorter bond length by 0.559Â and 0.415Â in comparison to the (b) isomer.
Discussion of dissociation energy:
Dissociation energy is the amount of energy required to break the hydrogen bonds. The dissociation energy for MMim-Cl (c) is +429kJmol-1 which is larger than the HMim-Cl (b) isomer, but smaller than the HMim-Cl (a) isomer. This suggests that MMim-Cl has stronger hydrogen bonding than HMim-Cl(b) likely because the chlorine is hydrogen bonded to two hydrogens. On the other hand, MMim-Cl has weaker hydrogen bonding than HMim-Cl(b).
Scan of HMim-Cl(a)
HMim-Cl (a) scan log file: Media: VDL_A_HMIMCL_IONPAIR_RIGID_SCAN.LOG
A plot of the rigid scan of the optimised HMim-Cl (a):
Discussion about the curve:
This plot depicts the bonding interaction between the HMim+ and Cl- ions and how the potential energy changes as the N-H bond distance varies by 0.1Å increments along the N-Cl coordinate path.
The HMim-Cl and MeNH-Cl PES appear to follow a very similar shape. The lowest energy was found for the N-H distance of 1.2Å. The HMim-Cl scan follows a very similar path moving from 0.8Å to 1.2Å but begins to differ at different rates after 1.2Å forming a wider 'dip' at the bottom of the curve. It is observed that the relative energy for HMim-Cl is lower than the MeNH-Cl energy suggesting that the hydrogen bonds at a slightly longer length are more stable for HMim-Cl than than MeNH-Cl. Similarly to MeNH-Cl, when HMim-Cl is in its neutral form (Mim and HCl) without proton transfer from the Cl, it is unstable due to its high relative energy.
