NH3 molecule

Summary information

Calculation method	RB3LYP
Basis set	6-31G(d,p)
Final energy E(RB3LYP) in au	-56.55776873
RMS gradient norm in au	0.00000485
Point group	C3V

Item section

 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

Jmol of NH3

test molecule

The optimisation file is liked to File:YQC18 NH3 OPTF POP.LOG

Key structural information

N-H bond distance= 1.02 +/- 0.01Å

H-N-H bond angle= 106 +/- 1°

Display vibrations table

Table of vibration and intensities

wavenumber(cm-1)	1090	1694	1694	3461	3590	3590
symmetry	A1	E	E	A1	E	E
intensity(arbitary units)	145	13.6	13.6	1.06	0.271	0.271
image

1. 6 modes are expected from 3N-6 rule

2. Modes with wavenumbers both being 1694 cm-1 are degenerate. Modes with wavenumbers both being 3590 cm-1 are also degenerate.

3. Modes with wavenumber 1090, 1694 and 1694 cm-1 are bending vibrations. Modes with wavenumbers 3461, 3590 and 3590 cm-1 are "bond stretch" vibrations.

4. Mode with wavenumber 3461 cm-1 is highly symmetric.

5. Mode with wavenumber 1090 cm-1 is the "umbrella mode"

6. I would expect to see 2 bands in an experimental spectrum of gaseoous ammonia.

NBO charges

The charge on N atom is -1.125 and charge on H atom is 0.375. I would expect negative charge on N and positive charge on H. This is because N is more electronegative than H hence pulls electron density towards H.

N2 and H2 molecules

N2 molecule

Summary information

Calculation method	RB3LYP
Basis set	6-31G(d,p)
Final energy E(RB3LYP) in au	-109.52412868
RMS gradient norm in au	0.00000060
Point group	D∞h

Item section

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

Jmol of N2

test molecule

The optimisation file is liked to File:YQC N2 OPTF POP.LOG

Key structural information

Optimised N-N bond length= 1.11 +/- 0.01 Å

Optimised N-N bond angle= 180 +/- 1°

Display vibration table

Table of vibrations and intensities

wavenumber(cm-1)	2457
symmetry	SGG
intensity(arbitary units)	0.00
image

NBO charges

The charge on both N atom is 0.000

H2 molecule

Summary information

Calculation method	RB3LYP
Basis set	6-31G(d,p)
Final energy E(RB3LYP) in au	-1.17853936
RMS gradient norm in au	0.00000017
Point group	D∞h

Item section

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

Jmol of H2

test molecule

The optimisation file is liked to File:YQC H2 OPTF POP.LOG

Key stuctural information

Optimised H-H bond length = 0.74 +/- 0.01 Å

Optimised H-H bond angle = 180 +/- 1°

Display vibration table

Table of vibration and intensities

wavenumber(cm-1)	4466
symmetry	SGG
intensity(arbitary units)	0.00
image

NBO charges

The charge on both N atom is 0.000.

A mono-metallic TM complex that coordinates N2

molecule name	(Dinitrogen-N)-(2-(1-(2,6-di-isopropylphenylimino)ethyl)-6-(1-(2,6-di-isopropylphenyl)amidoehenyl)pyridine-N,N'N)-iron
unique identifier	COGBIK
N-N bond distance obtained(Å)	1.11
N-N bond distance in the complex(Å)	1.14
structure
Link to the structure	https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=COGBIK&DatabaseToSearch=Published

The N-N bond distance in the complex is longer than computational distance.

Experimental reason: After accepting electrons from N, Fe becomes very negative and stabilizes by donating 3d electrons into pi-antibonding orbitals on N atom. This shortens Fe-N bond hence elongates N-N bond. This is called 'synergic effect'.

Computational reason: Computational analysis errors

Haber-Bosch reaction energy calculation

E(NH3)= -56.5577687 a.u

2*E(NH3)= -113.1155375 a.u

E(N2)= -109.5241287 a.u

E(H2)= -1.1785394 a.u

3*E(H2)= -3.5356181 a.u

ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -146.5 kJ/mol

The ammonia product is more stable

My choice of small molecule: HCN

Summary table

Calculation method	RB3LYP
Basis set	6-31G(d.p)
Final energy E(RB3LYP) in au	-93.42458132
RMS gradient norm in au	0.00017006
Point group	C∞v

Item section

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

Jmol of HCN

test molecule

The optimisation file is liked to File:YQC HCN OPTF POP.LOG

Key strucutral information

Optimised C-H bond length= 1.07 +/- 0.01 Å

Optimised C-N bond length = 1.16 +/- 0.01 Å

Optimised H-C-N bond angle = 180 +/- 1°

Display vibrations table

Table of vibrations and intensities

wavenumber(cm-1)	2215	767	767	3480
symmetry	SG	PI	PI	SG
intensity(arbitary units)	2.05	35.3	57.3
image

NBO charges

The charge on N atom is -0.308

The charge on C atom is 0.073

The charge on H atom is 0.234

Molecular orbitals

1.

1s atomic orbital from nitrogen contributes to the MO. The MO is non-bonding. The MO is deep in energy. The MO is occupied and has no effect on bonding.

2.

2s atomic orbitals from carbon,nitrogen and 1s atomic orbital from hydrogen contribute to the MO. The MO is bonding. The MO is deep in energy. The MO is occupied and stabilizes the bonding.

3.

2s atomic orbitals from hydrogem and nitrogen and 2pz atomic orbital from carbon contribute to the MO. The MO is bonding. The MO is deep in energy. The MO is occupied and destabilizes the bonding.

4.

2py atomic orbitals from carbon and nitrogen contribute to the MO. The MO is bonding. The MO is in the LUMO. The MO is occupied and stabilizes the bonding.

5.

2py atomic orbitals from carbon and nitrogen contribute to the MO. The MO is antibonding. The MO is in the HOMO. The MO is unoccupied and therefore has no effect on bonding.

Independent work: Cl2 molecule

Summary table

Calculation method	RB3LYP
Basis set	6-31G(d.p)
Final energy E(RB3LYP) in au	-920.34987886
RMS gradient norm in au	0.0000251
Point group	D∞h

Item section

Item               Value     Threshold  Converged?
 Maximum Force            0.000043     0.000450     YES
 RMS     Force            0.000043     0.000300     YES
 Maximum Displacement     0.000121     0.001800     YES
 RMS     Displacement     0.000172     0.001200     YES

Jmol of Cl2

test molecule

The optimisation file is liked to File:YQC CL2 OPTF POP.LOG

Key structural information

Optimised Cl-Cl bond length= 2.04 +/- 0.01 Å

Optimised Cl-Cl bond angle= 180 +/- 1°

Display vibrations table

Table of vibration and intensities

Wavenumber(cm-1)	520
Symmetry	SGG
Intensity(arbitary units)	0.00
image

NBO charges

The charge on both Cl atom is 0.000.

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, however you have left all the jmol captions as the default “test molecule” this gives the reader no information.

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 have given a bond angle of 180 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

Your choice of small molecule 2.5/5

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, you have included the relevant information well done! Your explanations of MOs 1 and 3 are very good and clearly explained! On the charges you could have improved by explaining why each atom has a different charge in terms of the relative electronegativities of the elements. For MO 4 the C-H bond is strengthened but the N-C bond is weakened. You also seem to be confused on the terms HOMO and LUMO, have a look back in your lecture notes for those terms or show your tutor your wiki and ask them.

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

Do some deeper analysis on your results so far

You did an extra calculation on Cl2 well done!