Rep:Mod:01514934
NH3 molecule
Summary information
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
E(RB3LYP): -56.55776873 a.u.
RMS Gradient Norm: 0.00000485
Point Group: C3V
N-H bond length: 1.02 Å
N-H bond angle: 106°
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
Structure information
NH3 |
Mode Symmetry Wavenumber(cm-1) Intensity 1 A1 1090 145 2 E 1694 14 3 E 1694 14 4 A1 3461 1 5 E 3590 0 6 E 3590 0
Number of modes expected:6
Degenerate modes:1694 cm-1 and 3590 cm-1
Bending modes:1090 cm-1 and 1694 cm-1
Stretching modes:3461 cm-1 and 3590 cm-1
Highly symmetric mode: 3461 cm-1
Umbrella mode:3461 cm-1
Number of bands expected to see in an experimental spectrum of gaseous ammonia: 2
Charge on N atom:-1.125
Charge on H atom:+0.375
Expected charge on N was -3 and that on H was +1
Link to log file:File:SLI NH3 OPTF POP.LOG
N2 molecule
Summary information
Calculation method: RB3LYP
Basis set: 6-31G(d,p)
Final energy E(RB3LYP): -109.52412868 a.u.
RMS gradient: 0.00000060 a.u.
Point group of the molecule: D*H
N-N bond distance: 1.11 Å
N-N bond angle: 180°
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
Structure information
N2 molecule |
Mode Symmetry Wavenumber(cm-1) Intensity 1 SGG 2457 0
Number of modes expected: 1
Stretching mode: 2457 cm-1
Number of bands expected to see in an experimental spectrum of gaseous nitrogen: 0
Charge on nitrogen: 0
Mono-metallic TM complex that coordinates N2: DEKFUX
N-N bond length in the complex: 1.086(6) Å
The crystal structure and computational distances are slightly different, which are 1.09 Å and 1.11 Å respectively. Gaussian and Mercury use different calculation methods. Computational method has limited accuracy. The packing effect of the crystal shortens the N-N bond length. All of these could contribute to the slight difference in the bond lengths.
Link to log file:File:SLI N2 OPTF POP.LOG
H2 molecule
Summary information
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
H-H bond length: 0.74 Å
H-H bond angle: 180°
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
Structure information
H2 molecule |
Mode Symmetry Wavenumber(cm-1) Intensity 1 SGG 4466 0
Number of modes expected: 1
Stretching mode: 4466 cm-1
Number of bands expected to see in an experimental spectrum of gaseous hydrogen: 0
Charge on hydrogen: 0
Mono-metallic TM complex that coordinates H2: HINNUN
H-H bond length in the complex: 1.22(6) Å
The H-H bond length in the optimised H2 is 0.74 Å, which is shorter than the one in the transition metal complex. Longer bond means the bond is weaker. In the optimised H2, electron density is spread around the two hydrogen atoms. However, in the metal complex, the electron density is spread around the two hydrogen atoms and the transition metal. Therefore, the electron density between H-H in the complex is less dense than that in the optimised H2 molecule. The H-H bond in the complex is therefore longer.
Link to log file:File:SLI H2 OPTF POP.LOG
Haber-Bosch process
E(NH3)= -56.5577687 a.u.
2*E(NH3)= -113.1155370 a.u.
E(N2)= -109.5241287 a.u.
E(H2)= -1.1785394 a.u.
3*E(H2)= -3.5356182 a.u.
ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557901 a.u. = -146.5 kJ/mol
NF3 molecule
Summary information
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
E(RB3LYP): -354.07131066 a.u.
RMS Gradient Norm: 0.00006772 a.u.
Point Group: C3V
N-F bond length: 1.38 Å
N-f bond angle: 102°
Item Value Threshold Converged? Maximum Force 0.000082 0.000450 YES RMS Force 0.000063 0.000300 YES Maximum Displacement 0.000356 0.001800 YES RMS Displacement 0.000157 0.001200 YES
Structure information
NF3 |
Mode Symmetry Wavenumber(cm-1) Intensity 1 E 482 1 2 E 482 1 3 A1 644 3 4 E 931 208 5 E 931 208 6 A1 1063 40
Number of modes expected:6
Degenerate modes:482 cm-1 and 931 cm-1
Bending modes: 482 cm-1 and 644 cm-1
Stretching modes: 931 cm-1 and 1063 cm-1
Highly symmetric mode: 644 cm-1
Umbrella mode:644 cm-1
Number of bands expected to see in an experimental spectrum of gaseous NF3: 2
Charge on N atom:+0.660
Charge on F atom:-0.220
Expected charge on N was +3 and that on F was -1
Link to log file:File:SLI NF3 OPTF POP.LOG
MO diagrams
Four 2s valence AOs on each atom overlap to form MO 5. The MO is a bonding orbital, whose energy is -1.35879 au. It is in the LUMO/HOMO region. The MO is occupied.
Two 2s valence AOs on F3 and F4 overlap to form MO 6. The MO is an anti bonding orbital, whose energy is -1.23351 au. It is in the LUMO/HUMO region. The MO is occupied. MO 6 AND MO 7 are degenerate.
Three 2s valence AOs on each fluorine atom overlap to form MO 7. The 2s AOs on F3 AND F4 form a bonding orbital. This orbital forms an anti bonding orbital with the 2s AO on F2. Therefore, MO 7 is a mixture. It has energy of -1.23351 a.u. It is occupied. MO 6 AND MO 7 are degenerate.
Three 2p AOs on each fluorine overlap with one 2s AO on nitrogen to form MO 8. It has an energy of -0.81871 au. It is a mixture. It is in the LUMO/HUMO region. It is occupied.
Three 2s AOs on each fluorine atom and one 2p AO on the nitrogen atom overlap to form MO 9. MO 9 is a mixture, with an energry of -0.61990 au. It is in the LUMO/HUMO region. It is also occupied.
PF5 molecule
Summary information
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
E(RB3LYP): -840.67634601 a.u.
RMS Gradient Norm: 0.00010182
Point Group: D3H
P-F bond length: 1.57 Å in the equatorial plane and 1.60 Å in the axial plane
P-F bond angle: 90° in the equatorial plane and 120° in the axial plane
Item Value Threshold Converged? Maximum Force 0.000299 0.000450 YES RMS Force 0.000090 0.000300 YES Maximum Displacement 0.000868 0.001800 YES RMS Displacement 0.000269 0.001200 YES
PF5 |
Link to log file:File:SLI PF5 OPTF POP.LOG
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 0.5/1
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?
NO
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 - however the umbrella mode is not the one at 3461cm-1 but 1090cm-1. Additionally you missed WHY you expected the charges you stated based on an electronegativity argument.
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)
YES - however you stated a bond angle for diatomic molecules. To define a bond angle a minimum of 3 atoms is needed! You could have explained that the charges are 0 as the electronegativities are equal.
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?
NO - but you gave the unique identifiers.
Have you compared your optimised bond distance to the crystal structure bond distance?
YES
Haber-Bosch reaction energy calculation 0.5/1
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?
NO - you missed to interpret the value of the calculated reaction energy.
Your choice of small molecule 3.5/5
Have you completed the calculation and included all relevant information?
YES
Have you added information about MOs and charges on atoms?
You have done a good job of presenting this information, well done! You could have explained the charges using an electronegativity argument. You commented on the energies and the occupied?unoccupied state correctly. However, except for MO5 you description of bonding/anti-bonding MOs are incorrect. A node does not necessarily mean it is an anti-bonding orbital (e.g. MO MO6 is a bonding orbital). Your description of contributing MOs are not correct overall (e.g. for MO6 and 7 you underestimated the influence of the 2p-orbitals on N.)
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 - well done!
Do some deeper analysis on your results so far