NH3 molecule

Structural Optimisation Information

File:DLK18 OPT NH3.LOG

Optimised NH3 molecule

Optimised structure information: Molecule: Ammonia (NH3)

Calculation Method: RB3LYP

Basis set:6-31G(d,p)

Final energy E(RB3LYP): -56.558 a.u

RMS gradient: 0.00000485

Point group: C3v

Optimised H-N-H angle : 106°

Optimised N-H bond distance: 1.02 Å


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

Vibrations

Vibrations
	Vibration 1	Vibration 2	Vibration 3	Vibration 4	Vibration 5	Vibration 6
wavenumber cm-1	1090	1694	1694	3461	3590	3590
symmetry	A1	E	E	A1	E	E
intensity arbitrary units	145	14	14	1.06	0.27	0.27
image	]

Vibrational Information:

Expected modes for ammonia: 6

Degenerate modes: 1964 and 3590 cm-1

Bending vibrations: 1090 and both 1694 cm-1

Stretching vibrations: 3461 and 3590 cm-1

Highly symmetric mode: 3461 cm-1

Umbrella mode: 1090 cm-1

Expected bands in spectrum of ammonia: 2

Charge Distribution

Charge on N atom: -1.1

Charge on H atom: 0.4

You would expect a negative charge on the N atom and a slightly positive charge on the H atom due to the difference in electronegativities, N being far more electronegative.

N2 Molecule

Structural Optimisation information

Molecule: Nitrogen (N2)

Calculation Method: RB3LYP

Basis set:6-31G(d,p)

Final energy E(RB3LYP): -109.5 a.u

RMS gradient: 0.00000011 a.u

Point group: D∞h

Optimised N-N bond distance: 1.11 Å

Optimised N-N bond angle: 180°

File:DLK18 OPT N2.LOG

Optimised N2 molecule

        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
 Predicted change in Energy=-1.115764D-14
 Optimization completed.

Vibrations

Vibrational Information:

Wavenumber: 2457.3 cm-1

Intensity arbitrary units: 0

Symmetry: SGG

Number of bands: 0 as there is no change in dipole moment, so will not appear in IR spectrum.

Charge Distribution

Charge on N atom = 0

N2 and a mono metallic TM complex

Unique Identifier : VEJSOV File:VEJSOV dlk18.mol

Optimised N2 molecule

N-N bond length in this Transition metal complex: 1.12 Å.

N-N bond length in computational structure: 1.11 Å.

As expected, the bond N-N bond length is slightly larger when bonded to the transition metal complex because of the extra bonding to the transition metal. The extra bond being formed means the orbitals from the nitrogen atom are now interacting with the d orbital of the transition metal, lowering the electron density between the two N atoms, decreasing the bond strength and hence increasing the bond length. However the computational structure is based on theory only whereas the value from the complex is experimental, this must be taken into account especially considering the difference is only 0.01Å, which could be insignificant and due to computational error.

H2 molecule

Structural Optimisation information

File:DLK18 H2 OPT.LOG

Optimised H2 molecule

Calculation Method: RB3LYP

Basis set:6-31G(d,p)

Final energy E(RB3LYP): -1.179 a.u

RMS gradient: 0.00000017 a.u

Point group: D∞h

Optimised H-H bond distance: 0.74 Å

Optimised 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
 Predicted change in Energy=-1.164080D-13
 Optimization completed.

Vibrations

Vibrational Information:

Vibration:4465.7 cm-1

Symmetry:SGG

Intensity arbitrary units: 0

Number of bands: 0 as there is no change in dipole moment, so will not be IR active.

Charge distribution

Charge on H atom: 0

The Haber-Bosch process

N2 + 3H2 -> 2NH3

This process is used to produce Ammonia - used for fertilisers- on an industrial scale from N2 gas and H2 gas. Using the data from the optimised structures, we can calculated associated energy values for this equation.

E(NH3)= -56.55777 a.u

2*E(NH3)= -113.1154 a.u

E(N2)= -109.52413 a.u

E(H2)= -1.17854 a.u

3*E(H2)= -3.53562 a.u

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05565 a.u

= -146.1 kJ/mol (by x 2625.5)

NF3 Molecule

File:NF3 DLK18.LOG

Optimised NF3 molecule

Structural Optimisation information

Molecule: Nitrogen Trifluoride (NF3)

Calculation Method: RB3LYP

Basis set:6-31G(d,p)

Final energy E(RB3LYP): -354.07 a.u

RMS gradient: 0.000068 a.u

Point group: C3v

Optimised F-N-F angle : 101.9°

Optimised N-F bond distance: 1.38 Å


         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
 Predicted change in Energy=-4.598548D-08
 Optimization completed.

Vibrations

Vibrations
	Vibration 1	Vibration 2	Vibration 3	Vibration 4	Vibration 5	Vibration 6
wavenumber cm-1	482	482	644	931	931	1063
symmetry	E	E	A1	E	E	A1
intensity arbitrary units	0.52	0.52	2.76	208.28	208.28	40.0

Vibrational Information:

Expected modes for NF3: 6

Degenerate modes: 482 and 931 cm-1

Bending vibrations: 482 (not clear cut, seems like one fluorine atom is stretching whilst 2 are bending) and 644 cm-1

Stretching vibrations: 1063 and 931 cm-1

Most symmetric vibration: 644 cm-1

Umbrella vibration: 644 cm-1

Number of bands in spectrum: 2

Charge Distribution

Charge on N atom: 0.66

Charge on F atom: -0.22

MO Diagrams

MO Diagrams
	MO 5	MO 6	MO 7	MO 8	MO 9
MO image		]		]	]

MO 5: Complete overlap of s A0s from all F atoms and N, forming bonding MOs. This particular bonding MO is the lowest energy out of all the MO images, because it has the most complete, sigma overlap.

MO 6: The s AOs of F4 and F3 atoms are involved in this antibonding MO, this is visible as there is no overlap between the two AOs and a node is present.

MO 7: Overlap of s AOs on F3 and F4 atom to form a bonding MO, whilst F2 s AO is antibonding. This image is therefore a mix of antibonding and bonding MO characteristics.

MO 8: This image shows contribution from both s and p atomic orbitals to form this MO. Contribution of p atomic orbitals from F atoms overlapping with s atomic orbital of N to form bonding MO. Assumed it was not antibonding from all F and N s atomic orbitals because the electron density on the Nitrogen orbital is larger, suggesting p orbital contribution from F atoms.

MO 9: This image shows a mixture of antibonding and bonding MO character, and also a contribution from both s and p atomic orbitals. F2 And N atoms' p AOs are overlapping to form bonding MO (pi), whereas F3 and F4 s AO are antibonding. This is high in energy as there is not only antibonding character,the bonding character comes from p AOs (form pi MOs) , which do not produce an as low energy overlap as s AOs (form sigma MOs)

PF5 molecule

File:DLK PF5.LOG

Optimised PF5 molecule

Calculation Method: RB3LYP

Structural optimisation summary:

Calculation Method: RB3LYP

Basis set:6-31G(d,p)

Final energy E(RB3LYP): -840.7 a.u

RMS gradient: 0.00010 a.u

Structural Information summary:

Point group: D3h

Optimised F-P-F angle : 90° and 120° in the axial and equatorial planes respectively.

Optimised P-F bond distance: 1.60 Å in axial plane and 1.57 Å in the equatorial plane.

2 angles and 2 bond lengths were found due to the Trigonal Bipyramid shape of the molecule.

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
 Predicted change in Energy=-2.770927D-07
 Optimization completed.

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 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 0/0.5

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 - You missed to include a links to the crystal structure. Referencing is important! However you included the unique identifier.

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

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 should have explained the charges using an electronegativity argument. You cannot describe a MO as a combination of bonding and anti-bonding. Additionally you got confused about the meaning of bonding/anti-bonding and non-bonding. Just because a MO has a node it is not necessarily anti-bonding! For example MO6 and 7 are bonding MOs and not anti-bonding ones! You tried to identify the Mos contributing to the MOs. However you missed to state the principal quantum number to make your discussion easier to follow. Besides you did not get all contributing Mos right (e.g. for MO6 there is a contribution of the 2p orbital of N to the MO) Except for the MO lowest in energy you missed to comment on the relative energy and if the MOs are occupied/unoccupied.

MO7 is actually a bonding MO between the sulpher 3p and hydrogen 1s, the node in the p orbital doesn't mean it is not a bonding interaction.

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