Rep:Mod:madl123
NH3 Molecule
Optimisation
| Optimised N-H bond distance | 1.02 Å |
| Optimised H-N-H bond angle | 37° |
| Calculation method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy, E(RB3LYP) | -56.55776873 au |
| RMS gradient | 0.00000485 au |
| Point group | C3V |
| 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 |
Optimised Molecule |
The completed optimisation file is linked here.
Vibrations
| Wavenumber (cm-1) | Symmetry | Intensity (arbitrary units) | Image |
|---|---|---|---|
| 1090 | A1 | 145 | 
|
| 1694 | E | 14 | 
|
| 1694 | E | 14 | 
|
| 3461 | A1 | 1 | 
|
| 3590 | E | 0 | 
|
| 3590 | E | 0 | 
|
The expected number of modes from the 3N-6 rule is 3(4)-6 = 6 as there are 4 atoms in the molecule (N = 4).
The modes at 1694cm-1 and 3590cm-1 are degenerate - they have the same energy.
The "bending" vibrations are at 1090cm-1 and 1694cm-1 , and the "bond stretch" vibrations are at 3461cm-1 and 3590cm-1 - the "bending" vibrations occur at lower wavenumbers.
The mode at 3461cm-1 is highly symmetric.
The mode at 1090cm-1 is known as the "umbrella" mode - all the displacement vectors point in the same direction
In an experimental spectrum of gasesous ammonia, you would expect to see two bands, one for the mode at 1090cm-1 and one for the modes at 1694cm-1 (the two bands overlap as they have the same wavenumber), as only the "bending" vibrations would produce a change in dipole moment.
Charge Analysis
N-charge = -1.125
H-charge = 0.375
You would expect N to have a negaitve charge and H a positive charge due to the substantial electronegativity difference between the N and H atoms - N is more electronegative than H so draws the electron density towards itself, becoming more negative whilst leaving the H atoms more positive, creating a permanent dipole.
N2 Molecule
Optimisation
| Optimised N-N bond distance | 1.11 Å |
| Calculation method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy, E(RB3LYP) | -109.52412868 au |
| RMS gradient | 0.00000001 au |
| Point group | D*H |
| 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 | 0.000000 | 0.001200 | YES |
Optimised Molecule |
The completed optimisation file is linked here.
Vibrations
Display Vibrations:
| Wavenumber (cm-1) | Symmetry | Intensity (arbitrary units) | Image |
|---|---|---|---|
| 2457 | SGG | 0 | 
|
The expected number of modes from the 3N-5 rule is 3(2)-5 = 1 as there are 2 atoms in the molecule (N = 2).
The mode is a "bond stretch" vibration.
In an experimental spectrum of gaseous nitrogen, you would not expect to see any bands because the single "bond stretch" mode does not result in a change in dipole.
Charge Analysis
N-charge = 0.0000
N2 is a homonuclear diatomic molecule - both the nitrogen atoms share the same number of electrons and have the same electronegativity therefore there is no dipole and the charge on each atom is 0.
Mono-metallic Transition Metal Complex - AFUXEH
N-N bond distance = 1.09 Å.
The N-N bond distance in the crystal structure (1.09 Å) is shorter than the optimised computational N-N bond distance (1.11 Å) therefore the bonding between the nitrogen atoms is stronger in the mono-metallic compound than in the homonuclear diatomic molecule. The experimental value, shown for the crystal structure, will also be different to the computed bond distance due to inaccuracies and approximations in the computational method which may account for the difference in bond distances (rather than bond strength differences).
The 3D structure can be found here.
H2 Molecule
Optimisation
| Optimised H-H bond distance | 0.743 Å |
| Calculation method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy, E(RB3LYP) | -1.17853936 au |
| RMS gradient | 0.00000017 au |
| Point group | D*H |
| 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 |
Optimised Molecule |
The completed optimisation file is linked here.
Vibrations
| Wavenumber (cm-1) | Symmetry | Intensity (arbitrary units) | Image |
|---|---|---|---|
| 4466 | SGG | 0 | 
|
The expected number of modes from the 3N-5 rule is 3(2)-5 = 1 as there are 2 atoms in the molecule (N = 2).
The mode is a "bond stretch" vibration.
In an experimental spectrum of gaseous hydrogen, you would not expect to see any bands because the single "bond stretch" mode does not result in a change in dipole.
Charge Analysis
H-charge = 0.0000
H2 is a homonuclear diatomic molecule - both the hydrogen atoms share the same number of electrons and have the same electronegativity therefore there is no dipole and the charge on each atom is 0.
The Haber-Bosch Process
N2 + 3H2 -> 2NH3
| E (NH3) = | -56.55776873 au |
| 2 * E (NH3) = | -113.1155375 au |
| E (N2) = | -109.52412868 au |
| E (H2) = | -1.17853936 au |
| 3 * E (H2) = | -3.53561808 au |
| ΔE = 2 *E (NH3) - [E (N2) + 3 * E (H2)] = | -0.05579074 au |
| ΔE (kJ mol-1) = ΔE (au) * 2625.5 = | -146.4785879 kJ mol-1 |
| ΔE (1.d.p) = | -146.5 kJ mol-1 |
Therefore, the energy for converting hydrogen and nitrogen gas into ammonia is -146.5 kJ mol-1. The value is negative therefore this is an exothermic process meaning the ammonia product is thermodynamically more stable than the gaseous reactants (ammonia has a lower energy than the gaseous reactants, nitrogen and hydrogen, and so is more stable).
Chosen Molecule - CH4
Optimisation
| Optimised C-H bond distance | 1.09 Å |
| Optimised H-C-H bond angle | 109° |
| Calculation method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy, E(RB3LYP) | -40.52401404 au |
| RMS gradient | 0.00003263 au |
| Point group | TD |
| Item | Value | Threshold | Converged? |
|---|---|---|---|
| Maximum Force | 0.000063 | 0.000450 | YES |
| RMS Force | 0.000034 | 0.000300 | YES |
| Maximum Displacement | 0.000179 | 0.001800 | YES |
| RMS Displacement | 0.000095 | 0.001200 | YES |
Optimised Molecule |
The completed optimisation file is linked here.
Vibrations
| Wavenumber (cm-1) | Symmetry | Intensity (arbitrary units) | Image |
|---|---|---|---|
| 1356 | T2 | 14 | 
|
| 1356 | T2 | 14 | 
|
| 1356 | T2 | 14 | 
|
| 1579 | E | 0 | 
|
| 1579 | E | 0 | 
|
| 3046 | A1 | 0 | 
|
| 3162 | T2 | 25 | 
|
| 3162 | T2 | 25 | 
|
| 3162 | T2 | 25 | 
|
The expected number of modes from the 3N-6 rule is 3(5)-6 = 9 as there are 5 atoms in the molecule (N = 5).
The modes at 1356cm-1, 1579cm-1, and 316cm-12 are degenerate - they have the same energy.
The "bending" vibrations are at 1356cm-1 and 1579cm-1 , and the "bond stretch" vibrations are at 3046cm-1 and 3162cm-1 - the "bending" vibrations occur at lower wavenumbers.
The mode at 3046cm-1 is highly symmetric.
In an experimental spectrum of gasesous methane, you would expect to see two bands, one for the modes at 1356cm-1 and one for the modes at 1579cm-1 (bands at the same wavenumber overlap), as only the "bending" vibrations would produce a change in dipole moment.
Charge Analysis
C-charge = -0.930
H-charge = 0.233
You would expect C to have a negative charge and H a positive charge due to the electronegativity difference between the C and H atoms - C is more electronegative than H so draws the electron density towards itself, becoming more negative whilst leaving the H atoms more positive, creating a permanent dipole.
Molecular Orbitals
| Molecular Orbital | Energy (au) | Character |
|---|---|---|
 |
-10.16707 | This is the 1s atomic orbital of carbon, occupied by two electrons. The AO is deep in energy (much deeper than the MOs formed from valence shell AOs - it is the lowest energy orbital) and is not involved in bonding. |
 |
-0.69041 | This is the bonding MO formed from the overlap of the 2s AO of carbon and the 1s AOs of hydrogen, occupied by two electrons. This is the second lowest energy MO but its energy is much higher (in the HOMO/LUMO region) because it is a valence MO (formed from the overlap of two AOs) and is very involved in the chemical bonding - the formation of this MO results in a σ-bond between carbon and hydrogen. |
 |
-0.38831 | This is the bonding MO formed from the overlap of a 2p AO of carbon and the 1s AOs of hydrogen atom, occupied by two electrons. It is the HOMO (highest occupied molecular orbital). There are two further bonding MOs formed from the 2p AOs of carbon and 1s AOs of hydrogen with the same energy, so the three MOs are degenerate. The formation of this MO results in a σ-bond between carbon and hydrogen. |
 |
0.11824 | This is the anti-bonding MO formed from the overlap of the 2s AO of carbon and the 1s AOs of hydrogen, and it is unoccupied and so is not involved in bonding. This is the LUMO (lowest unoccupied molecular orbital). It is so high in energy that it has positive energy. |
 |
0.17677 | This is the anti-bonding MO formed from the overlap of a 2p AO of carbon and the 1s AOs of hydrogen, and it is unoccupied and so is not involved in bonding. There are two further anti-bonding MOs formed from the 2p AOs of carbon and 1s AOs of hydrogen with the same energy so the three MOs are degenerate. This MO is so high in energy that it has positive energy. |
Independence - HCN
Optimisation
| Optimised C-H bond distance | 1.07 Å |
| Optimised C-N bond distance | 1.16 Å |
| Optimised H-C-N bond angle | 180° |
| Calculation method | RB3LYP |
| Basis set | 6-31G(d,p) |
| Final energy, E(RB3LYP) | -93.42458132 au |
| RMS gradient | 0.00017006 au |
| Point group | C*V |
The C-N bond distance (1.16 Å) is smaller than the C-H bond distance - N is a larger atom than H so the valence electrons are in a larger orbital (2p compared to 1s).
The C-H bond distance in HCN (1.07 Å) is smaller than the C-H bond distance in CH4 (1.09 Å), therefore the C-H bond is stronger in HCN compared to CH4.
| Item | Value | Threshold | Converged? |
|---|---|---|---|
| Maximum Force | 0.000370 | 0.000450 | YES |
| RMS Force | 0.000255 | 0.000300 | YES |
| Maximum Displacement | 0.000676 | 0.001800 | YES |
| RMS Displacement | 0.000427 | 0.001200 | YES |
Optimised Molecule |
The completed optimisation file is linked here.
Vibrations
| Wavenumber (cm-1) | Symmetry | Intensity (arbitrary units) | Image |
|---|---|---|---|
| 767 | PI | 35 | 
|
| 767 | PI | 35 | 
|
| 2215 | SG | 2 | 
|
| 3480 | SG | 57 | 
|
The expected number of modes from the 3N-5 rule is 3(3)-5 = 4 as there are 3 atoms in the molecule (N = 3).
The modes at 767cm-1 are degenerate - they have the same energy.
The "bending" vibrations are at 767cm-1, and the "bond stretch" vibrations are at 2215cm-1 and 3480cm-1 - the "bending" vibrations occur at lower wavenumbers.
The mode at 2215cm-1 is highly symmetric.
In an experimental spectrum of gasesous hydrogen cyanide, you would expect to see one band, for the modes at 767cm-1 (bands at the same wavenumber overlap), as only the "bending" vibrations would produce a change in dipole moment.
Charge Analysis
H-charge = 0.234
C-charge = 0.073
N-charge = -0.308
You would expect N to have a negative charge and C a positive charge due to the electronegativity difference between the C and N atoms - N is more electronegative than C so draws the electron density towards itself, becoming more negative whilst leaving C more positive, creating a permanent dipole. Similarly, C is more electronegative than H so draws the electron density towards itself, hence the less positive charge on C.
Marking
Note: All grades and comments are provisional and subject 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 received your grade from blackboard.
Wiki structure and presentation 0.5/1
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 - all your mol captions are 'Optimised Molecule' which is not too informative.
NH3 1/1
Have you completed the calculation and given a link to the file?
YES
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?
YES
Have you included answers to the questions about vibrations and charges in the lab script?
YES
N2 and H2 0.5/0.5
Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)
YES
Crystal structure comparison 0.5/0.5
Have you included a link to a structure from the CCDC that includes a coordinated N2 or H2 molecule?
YES
Have you compared your optimised bond distance to the crystal structure bond distance?
YES
Haber-Bosch reaction energy calculation 1/1
Have you correctly calculated the energies asked for? ΔE=2*E(NH3)-[E(N2)+3*E(H2)]
YES
Have you reported your answers to the correct number of decimal places?
YES
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?
YES
Your choice of small molecule 4/5
Have you completed the calculation and included all relevant information?
YES
Have you added information about MOs and charges on atoms?
YES
You could have labelled the first displayed MO as non-bonding. You could have analysed and explained the energetic order of the MOs.
Independence 1/1
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
YES - however the stretching vibration at 3480cm-1 has the highest intensity of all modes and therefore will be observed in a spectrum. Probably this is just a copy and paste mistake as you gave the correct numbers of expected bands.
Do some deeper analysis on your results so far