Rep:Mod:01493160
Molecular Modelling
NH3 Molecule
NH3 molecule |
| Molecule name | Ammonia |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| E(RB3LYP) | -56.55776873 a.u. |
| RMS Gradient Norm | 0.00000485 a.u. |
| Point Group | C3V |
| N-H bond length | 1.018 angstroms |
| H-N-H bond angle | 105.7 |
NH3 Item Table
Item Value Threshold Converged? Maximum Force 0.000004 0.000450 YES RMS Force 0.000004 0.000300 YES Maximum Displacement 0.000072 0.001800 YES RMS Displacement 0.000035 0.001200 YES
NH3 Display Vibration Table
Expected vibrational modes:6
Degenerate modes: 2,3 and 5,6
Bending vibrations:1,2 and 3
Stretching vibrations:4,5 and 6
Highly symmetric vibrations:4
'Umbrella' mode:4
Experimental spectrum bands expected:6
Vibrations
NH3 Frequency Analysis
| Wavenumber/cm**-1 | Symmetry | Intensity |
| 1090 | A1 | 145 |
| 1694 | E | 14 |
| 1694 | E | 14 |
| 3461 | A1 | 2 |
| 3590 | E | 1 |
| 3590 | E | 1 |
NH3 Charge Distribution
Nitrogen Charge:-1.125
Hydrogen's charge:0.375
N2 Molecule
N2 molecule |
| Molecule name | Nitrogen |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| E(RB3LYP) | -109.52412868 a.u. |
| RMS Gradient Norm | 0.00000060 a.u. |
| Point Group | D*H |
| N-N bond length | 1.111 angstroms |
N2 Item Table
Item Value Threshold Converged? Maximum Force 0.000001 0.000450 YES RMS Force 0.000001 0.000300 YES Maximum Displacement 0.000000 0.001800 YES RMS Displacement 0.000000 0.001200 YES
N2 Display Vibrations Table
Vibrations
N2 Frequency Analysis
Expected Vibrational Modes:1
| Wavenumber/cm**-1 | Symmetry | Intensity | Displacement vectors |
| 2457 | SGG | 0 | 
|
N2 Charge Distribution
H2 Molecule
H2 molecule |
| Molecule name | Hydrogen |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| E(RB3LYP) | -1.17853936 a.u. |
| RMS Gradient Norm | 0.00000017 a.u. |
| Point Group | D*H |
H2 Item Table
Item Value Threshold Converged? Maximum Force 0.000000 0.000450 YES RMS Force 0.000000 0.000300 YES Maximum Displacement 0.000000 0.001800 YES RMS Displacement 0.000001 0.001200 YES
H2 Display Vibrations Table
Vibrations
H2 Frequency Analysis
Expected Vibrational Modes:1
| Wavenumber/cm**-1 | Symmetry | Intensity |
| 4466 | SGG | 0 |
Transition Metal Complex
Comparing N-N triple bond lengths
The bond length in the optimized nitrogen diatomic molecule (1.11 angstroms) is recorded to be greater than the measured length of the bond in the complex (1.104 angstroms). The reason for the difference in bond length is due to the error associated with measuring bond lengths experimentally. As N2 is naturally a gas, to experiment to achieve a bond length it is needed to be in a crystaline form. Depending on the transition metal used, can cause different values of the bond length. Using a computational method gives a length, without taking into account outside factors, by treating it using a forcefield.
Energy Changes in production of Ammonia
| E(NH3) | 0.017 a.u. |
| 2E(NH3) | 0.035 a.u. |
| E(N2) | 0.360 a.u. |
| E(H2) | 0.166 a.u. |
| 3E(H2) | 0.498 a.u. |
| ΔE | -0.823 a.u. |
SH2 Molecule
SH2 molecule |
| Molecule name | Hydrogen Sulfide |
| Calculation Method | RB3LYP |
| Basis Set | 6-31G(d,p) |
| E(RB3LYP) | -399.39162414 a.u. |
| RMS Gradient Norm | 0.00012068 a.u. |
| Point Group | C2V |
| S-H bond length | 1.347 angstroms |
| H-S-H bond angle | 92.7 |
SH2 Item Table
Item Value Threshold Converged? Maximum Force 0.000175 0.000450 YES RMS Force 0.000145 0.000300 YES Maximum Displacement 0.000386 0.001800 YES RMS Displacement 0.000386 0.001200 YES
SH2 Display Vibrations Table
Vibrations
SH2 Frequency Analysis
Expected Vibrational Modes: 3
| Wavenumber/cm**-1 | Symmetry | Intensity | Displacement vectors |
| 1224 | A1 | 5 | 
|
| 2692 | A1 | 7 | 
|
| 2712 | B2 | 9 | 
|
SH2 Charge Distribution
Sulfur Charge:-0.312
Hydrogen Charge:0.156
SH2 Molecular Orbitals
Information
Of the molecular orbitals above 1,2 and 4 are examples of bonding orbitals, where as 3 and 5 are examples of anti-bonding orbitals.
Marking
Note: All grades and comments are provisional and subjecct to change until your grades are officially returned via blackboard. Please do not contact anyone about anything to do with the marking of this lab until you have recieved your grade from blackboard.
Wiki structure and presentation 1/1
Is your wiki page clear and easy to follow, with consistent formatting?
YES
Do you effectively use tables, figures and subheadings to communicate your work?
YES
NH3 0/1
Have you completed the calculation and given a link to the file?
NO - you missed to include a link to you .log file. This is important as we need it as a proof of your own work. Therefore the amount of marks that can be achieved is reduced by 1. However you included all other relevant data and displayed them in a useful way.
Have you included summary and item tables in your wiki?
YES
Have you included a 3d jmol file or an image of the finished structure?
YES
Have you included the bond lengths and angles asked for?
YES
Have you included the “display vibrations” table?
YES
Have you added a table to your wiki listing the wavenumber and intensity of each vibration?
YES
Did you do the optional extra of adding images of the vibrations?
NO
Have you included answers to the questions about vibrations and charges in the lab script?
YES
You identified the highly symmetric vibration correctly. However this stretching is not the socalled umbrella motion. If you have a look again at the animation you will realise mode 1 is comparable of the motion during opening an umbrella. You stated to expect 6 modes in the experimental spectrum. You correctly identified 2 pairs of degenerate modes. This reduces the number of modes to 4. The stretching modes are too low in intensity, so they are not visible in the experimental spectrum and only 2 bands are observed.
N2 and H2 0/0.5
Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)
NO - you missed to include a link to you .log file. This is important as we need it as a proof of your own work. Therefore the amount of marks that can be achieved is reduced by 1. You are displaying your data in a good way! But only showing them is not enough, make comments on that you expected before you conducted the calculations.
Crystal structure comparison 0/0.5
Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?
NO - You found a reasonable structure but referencing is important. By not giving a link we cannot trace back the data you have given.
Have you compared your optimised bond distance to the crystal structure bond distance?
YES - Your discussion is reasonable. But the error in measuring the crystal structure is not the overall reason for the difference. The point of being in solid state is more important. The last sentence of this section cannot applied to your calculation because you used Gaussian to perform electron density calculations. Forcefield calculations were part of the IMM1 lab.
Haber-Bosch reaction energy calculation 0/1
Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]
NO - The energies obtained in the prior calculations are correct. But you used wrong numbers in the energy calculation of the Haber Bosch Process (e.g. you used 0.017a.u. for NH3 but the value of your previous calculation is -56 Hartree.) This results in an error for the following calculations. However you displayed the values in a good way!
Have you reported your answers to the correct number of decimal places?
NO - For calculated energies the number of digital places should be within the range of 5 to 7.
Do your energies have the correct +/- sign?
YES
Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?
NO
Your choice of small molecule 2/5
Have you completed the calculation and included all relevant information?
NO - the.log file is missing, therefore you cannot get more than 4 marks for this section. But besides all other relevant information are given.
Have you added information about MOs and charges on atoms?
You could have explained the charges using an electronegativity argument and commented on the calculated vibrations. You missed to mention which MOs are involved in building the displayed MOs. As well information on their energies and if they are occupied or non-occupied are missing. Your conclusions regarding the bonding nature of the MOs are mostly correct. Only the first displayed MO is not a bonding one as you stated. It originates from a 2p orbital of S and does not interact with an AO of H at all. It is non-bonding.
Independence 0/1
If you have finished everything else and have spare time in the lab you could: Check one of your results against the literature, or Do an extra calculation on another small molecule, or Do some deeper analysis on your results so far
NO -no independent work was identified