Title

NH₃ molecule

N-H bond length = 1.02

H-N-H bond angle = 106

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -56.55777 a.u.

RMS Gradient Norm = 0.00000485 a.u.

Point Group = C3_V

 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

Predicted change in Energy=-5.986301D-10

test molecule

File:RP3218 NH3 OPTF POP.LOG

The N in the NH₃ molecule will have a negative charge, compared to the three Hydrogens as it is more electronegative than the hydrogens, therfore making it more electron withdrawing, hence a negative charge.

Wavenumber cm^-1	1090	1694	1694	3461	3590	3590
Symmetry	A1	E	E	A1	E	E
Intensity arbitrary units	145	14	14	1	0.3	0.3
Image

How many modes do you expect from the 3N-6 rule?

Which modes are degenerate (ie have the same energy)?

Which modes are "bending" vibrations and which are "bond stretch" vibrations?

Which mode is highly symmetric?

One mode is known as the "umbrella" mode, which one is this?

How many bands would you expect to see in an experimental spectrum of gaseous ammonia?

Expected modes = 6

Degenerate modes = The two modes of vibrations at 1694cm^-1 are degenerate and the two vibrations at 3590cm^-1

"Bending" vibrations = The vibrations at 1090cm^-1 , 1694cm^-1 and 1694cm^-1 are bending modes

"Bond stretch" vibrations = The vibrations at 3461cm^-1 , 3590cm^-1 and 3590cm^-1 are stretching modes

Highly symmetric mode = The highly symmetric mode is at 3461cm^-1

"Umbrella" mode = The umbrella mode is the 1090cm^-1 vibration

Number of bands in an experimental spectrum of gaseous ammonia = 3

N₂ molecule

N-N bond length = 1.11 Å

N-N bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -109.52412868

RMS Gradient Norm = 0.00000060

Point Group = D*H

 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
 
Predicted change in Energy=-3.401191D-13

test molecule

File:RPABC N2 OPTIMISE.LOG

Wavenumber cm^-1	2457
Symmetry	SGG
Intensity arbitrary units	0
Image

Below is a link for a mono-metallic TM complex that coordinates N₂.

[[1]]

The bond distance for N₂ was 1.11 Å when calculated, whilst the bond distance of the crystal structure in the above link is 1.13 Å ^[1]. The similarity is because of the similar bond strength. However the slight difference in distance is due to the withdrawal of electron density towards the Fe atom, reducing the bond order of the N-N bond, therefore making the bond weaker and longer. The bond distance found via the optimisation was an approximation, whilst the distance found via experimental means was different as the N₂ molecule was bound to an Fe complex.

My expectations for the charges on the N atoms are zero, as the two Nitrogen atoms have the same electron density and electronegativity, therefore a zero charge.

H₂ molecule

H-H bond length = 0.74 Å

H-H bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -1.17853936

RMS Gradient Norm = 0.00000017

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
 
Predicted change in Energy=-1.164080D-13

H2

File:RPAREKH H2 OPTF POP.LOG

Wavenumber cm^-1	4466
Symmetry	SGG
Intensity arbitrary units	0
Image

My expectations for the charges on the H atoms are zero, as the two hydrogen atoms have the same electron density and electronegativity, therefore a zero charge.

Haber-Bosch Process

E(NH₃)= -56.55777 a.u.

2*E(NH₃)= -113.11554 a.u.

E(N₂)= -109.52412868 a.u.

E(H₂)= -1.17853936 a.u.

3*E(H₂)= -3.53561808 a.u.

ΔE= 2*E(NH₃)-[E(N₂)+3*E(H₂)]= -0.05580 a.u.

ΔE= -146.5 KJ/mol

The more stable substance is the NH₃ as this is an exothermic reaction, therefore the NH₃ is at a lower energy state, which means it has a lower energy than both the reactants combined.

O₂ Molecule

O-O bond length = 1.22 Å

O-O bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -150.25742435 a.u.

RMS Gradient Norm = 0.00000974 a.u.

Point Group = SGG

 Item               Value     Threshold  Converged?

Maximum Force            0.000017     0.000450     YES
 
RMS     Force            0.000017     0.000300     YES
 
Maximum Displacement     0.000010     0.001800     YES
 
RMS     Displacement     0.000015     0.001200     YES
 
Predicted change in Energy=-1.739381D-10

test molecule

File:RPAREKH O2 OPTF POP.LOG

Wavenumber cm^-1	1643
Symmetry	SGG
Intensity arbitrary units	0
Image

My expectations for the charges on the H atoms are zero, as the two hydrogen atoms have the same electron density and electronegativity, therefore a zero charge.

MO number and type	σ_1s	σ*_1s	σ_2s	σ*_2s	σ_{2p_z}
MO photo
AOs which contribute to MOs	Two 1s	Two 1s	Two 2s	Two 2s	Two 2p (2p_x)
Is MO Bonding, Antibonding or Both?	Bonding	Antibonding	Bonding	Antibonding	Bonding
Depth of MO energy in HOMO/LUMO region	-19.31 (Very Deep in Energy)	-19.31 (Very Deep in Energy)	-1.28 (Higher in Energy than 1s AOs, this is a valence energy level)	-0.80 (Valence energy level therefore high in Energy than 1s AOs and 2s bonding AO)	-0.53 (Valence energy level therefore high in energy)
Is MO Occupied or Unoccupied?	Occupied	Occupied	Occupied	Occupied	Occupied
Effect of MO on Bonding	Little. This has only a small contibution to bonding since the AOs are so deep in energy and so hardly overlap at all, also they are held tightly to the nuclei.	Little, for same reason as on left, due to being very low in energy therefore poor overlap.	Large, since the 2s AOs are large hence there is strong overlap, which is why these AOs are valence AOs due to the increase in enrgy compared to the 1s AOs.	Large, for the same reason as on the left. The bonding is so extensive, that it extends throughout the bond, hence a strong overlap. As this is an antibonding orbital, it will be higher in energy therefore less stable than a bonding MO. Due to the increased overlap of orbitals, the energy difference between the bonding and antibonding orbitals is larger.	Large, since this MO is formed via the head-on overlap of two 2p_z AOs. The fact that the energy gap between the 2s AOs and 2p AOs of O₂ is large, means that s-p mixing does not occur, therefore the shape of this MO is not distorted. In this case the bond order would not be affected if O₂ did participate in s-p mixing.

CO₂

C-O bond length = 1.17 Å

O-C-O bond angle = 180°

Calculation Method = RB3LYP

Basis Set = 6-31G(d,p)

E(RB3LYP) = -188.58093945 a.u.

RMS Gradient Norm = 0.00001154 a.u.

Point Group = SGG

 Item               Value        Threshold  Converged?
 
Maximum Force            0.000024     0.000450     YES
 
RMS     Force            0.000017     0.000300     YES
 
Maximum Displacement     0.000021     0.001800     YES
 
RMS     Displacement     0.000015     0.001200     YES
 
Predicted change in Energy=-5.259645D-10

test molecule

File:RPAREKH CO2 OPTF POP.LOG

Wavenumber cm^-1	640	640	1372	2436
Symmetry	PTU	PTU	SGG	SGU
Intensity arbitrary units	30.7	30.7	0	546
Image

The two Oxygen atoms in the CO₂ molecule will have a negative charge, compared to the Carbon as they are more electronegative than the Carbon, therfore making it more electron withdrawing, hence a negative charge.

↑ (1) Kuriyama, S.; Arashiba, K.; Nakajima, K.; Matsuo, Y.; Tanaka, H.; Ishii, K.; Yoshizawa, K.; Nishibayashi, Y. Nature Communications 2016, 7.

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?

You didn't use the built in subheadings which automatically generate a contents page, this makes it much easier for a reader to navigate. You have left the jmol captions as the default “test molecule” this gives the reader no information.

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 most answers are correct. However there are only 2 visible peaks in the spectra of NH3, due to the low intensity of the other 2 peaks. (See infrared column in vibrations table.)

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 5/5

Have you completed the calculation and included all relevant information?

YES

Have you added information about MOs and charges on atoms?

YES, good explanations, well done!

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

You did an extra calculation, well done.

Do some deeper analysis on your results so far

[Distance-1] (1) Kuriyama, S.; Arashiba, K.; Nakajima, K.; Matsuo, Y.; Tanaka, H.; Ishii, K.; Yoshizawa, K.; Nishibayashi, Y. Nature Communications 2016, 7.

[1]