Rep:Mod:MTC3018
NH3 molecule
Calculation method: B3LYP
Basis set: 6-31G(d,p)
Point group: C3V
Final energy E(RB3LYP): -56.55776873 a.u.
RMS gradient: 0.00000485 a.u.
optimised N-H bond distance: 1.02 A
optimised H-N-H bond angle: 105°
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 molecule |
Vibrational Analysis
Number of modes expected from 3N-6 rule: 6
Degenerate modes: 2&3, 5&6
Bending vibrations: 1, 2, 3
Stretching vibrations: 4, 5, 6
Highly symmetric mode: 4
"Umbrella" mode: 1
Number of bands expected to see in an experimental spectrum of gaseous ammonia: 4
| Wavenumber cm-1 | Symmetry | Intensity |
|---|---|---|
| 1090 | A1 | 145 |
| 1694 | E | 13 |
| 1694 | E | 13 |
| 3461 | A1 | 1 |
| 3590 | E | 0 |
| 3590 | E | 0 |
Charge Analysis
Charge on N atom: -1.125
Charge on H atoms: 0.375
A negative charge is expected on the N atom and positive charges on H atoms, as N is more electronegative than H
N2 molecule
Calculation method: B3LYP
Basis set: 6-31G(d,p)
Point group: D∞h
Final energy E(RB3LYP): -109.52359111 a.u.
RMS gradient: 0.02473091 a.u.
Bond length: 1.1 A
Bond angle: 0°
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 molecule |
Vibrational Analysis
| Wavenumber cm-1 | Symmetry | Intensity |
|---|---|---|
| 2457 | SGG | 0 (no change in dipole moment) |
Charge Analysis
Charge on N atom: 0 (The molecule is nonpolar)
H2 molecule
Calculation method: B3LYP
Basis set: 6-31G(d,p)
Point group: D∞h
Final energy E(RB3LYP): -1.17853936 a.u.
RMS gradient: 0.00000017 a.u.
Bond length: 0.74 A
Bond angle: 0°
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 molecule |
Vibrational Analysis
| Wavenumber cm-1 | Symmetry | Intensity |
|---|---|---|
| 4465 | SGG | 0 (no change in dipole moment) |
Charge Analysis
Charge on H atom: 0 (The molecule is nonpolar)
N2 TM complex
Unique identifier: BIRQEA
N-N bond distance from optimisation: 1.105 A
N-N bond distance in the structure: 1.124 A
The distances are different, as the first one results from a computational optimisation method and the second one is experimentally measured. Secondly, the bond in the TM complex is different due to the interactions of the electrons in the bond with the metal, which makes the electron density in the bond lower and therefore the attraction lower, resulting in a longer bond.
Haber-Bosch process
E(NH3)=-56.55776873
2*E(NH3)=-113.11553746
E(N2)=-109.52359111
E(H2)=-1.17853936
3*E(H2)=-3.53561808
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]=-0.05632827 a.u.
ΔE(kJ/mol)=-147.9 kJ/mol
The ammonia product is more stable, as this is an exothermic reaction.
SH2 molecule
Calculation method: B3LYP
Basis set: 6-31G(d,p)
Point group: C2v
Final energy E(RB3LYP): -399.39162414 a.u.
RMS gradient: 0.00012068 a.u.
Bond length: 1.35 A
Bond angle: 93°
Item Value Threshold Converged? Maximum Force 0.000175 0.000450 YES RMS Force 0.000145 0.000300 YES Maximum Displacement 0.000472 0.001800 YES RMS Displacement 0.000386 0.001200 YES
This table shows that the values of the force and displacement resulted after optimisation are below the threshold, which means that the energy of the optimised molecule is close to the lowest it can get, as the force (gradient) is close to 0. Therefore, the optimisation was successful.
SH2 molecule |
Vibrational Analysis
Number of modes expected from 3N-6 rule: 3
Degenerate modes: No degenerate modes
Bending vibrations: 1
Stretching vibrations: 2, 3
Number of bands expected to see in an experimental spectrum of gaseous SH2: 3
| Mode | Wavenumber cm-1 | Symmetry | Intensity |
|---|---|---|---|
| 1 | 1224 | A1 | 5 |
| 2 | 2692 | A1 | 7 |
| 3 | 2712 | B2 | 9 |
Charge Analysis
Charge on S atom: -0.312
Charge on H atoms: 0.156
(The negative charge is on S, as it is more electronegative than H.)
Molecular orbitals
Energy: High (This orbital is the HOMO)
Bonding/Antibonding: Nonbonding
Contributing AOs: 3p (S)
Occupied/Unoccupied: Occupied
Effect on bonding: They interact with orbitals in nucleophilic reactions, attacking an electrophile.
Energy: Deep
Bonding/Antibonding: Nonbonding
Contributing AOs: 2s (S)
Occupied/Unoccupied: Occupied
Effect on bonding: No effect on bonding, the orbital is too low in energy (core) to contribute to bonding.
Energy: Deep
Bonding/Antibonding: Bonding
Contributing AOs: 3s (S), 1s (H), 1s (H)
Occupied/Unoccupied: Occupied
Effect on bonding: Highest bonding character. It is deep in energy so it doesn't participate to chemical reactions.
Energy: High
Bonding/Antibonding: Bonding
Contributing AOs: 3p (S), 1s (H), 1s (H)
Occupied/Unoccupied: Occupied
Effect on bonding: Bonding character with orbitals out of phase.
Energy: High (This orbital is the LUMO)
Bonding/Antibonding: Antibonding
Contributing AOs: 3p (S), 1s (H), 1s (H)
Occupied/Unoccupied: Unoccupied
Effect on bonding: They accommodate electrons from nucleophilic species.
SbF5 molecule
Calculation method: B3LYP
Basis set: LANL2DZ
Point group: D3H
Final energy E(RB3LYP): -504.7057579 a.u.
RMS gradient: 0.0174457 a.u.
Bond length: 1.90 A (axial), 1.89 (ecuatorial)
Bond angle: 90°, 120° (structure: trigonal bipyramidal)
Item Value Threshold Converged? Maximum Force 0.000143 0.000450 YES RMS Force 0.000059 0.000300 YES Maximum Displacement 0.000589 0.001800 YES RMS Displacement 0.000248 0.001200 YES
SH2 molecule |
Vibrational Analysis
Number of modes expected from 3N-6 rule: 12
Degenerate modes: 1&2, 3&4, 5&6, 11&12
Bending vibrations: 1, 2, 3, 4, 5, 6, 7
Stretching vibrations: 8, 9, 10, 11, 12
Number of bands expected to see in an experimental spectrum of gaseous SH2: 4
Charge Analysis
Charge on Sb atom: 3.040
Charge on H atoms: -0.606 (ecuatorial), -0.612 (axial)
(The negative charge is on F, as it is more electronegative than Sb. The axial and ecuatorial F atoms are in 2 different chemical environments, with the axial atoms further away from the Sb atom, so they experience less attraction.)
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 recieved 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 - overall this is good. However you have a few inconsistencies in formatting which make it harder to follow your work - random capitalisation, randon subheads are bolded, and some sentences lack punctuation.
NH3 0.5/1
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 - correct explanation of charges and most vibration questions were answered correctly.
However due to the low intensity of vibrations 4, 5 and 6 you only see two peaks in the IR spectrum.
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
However you have given a bond angle of 0 for N2 and H2, there are no bond angles in diatomic molecules. Bond angles involve exactly 3 atoms.
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 - correct explanation, well done!
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 - good summaries of the properties of the MOs. A little more detail on MOs 7 and 10 would have added a mark.
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
Do some deeper analysis on your results so far