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NH3 Optimisations

NH3 Summary

Molecule NH3
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -56.55776873 a.u.
RMS Gradient 0.00000485 a.u.
Point Group C3V
Optimised N-H Bond Length 1.02 Å
Optimised H-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

Predicted change in Energy = -5.986280D-10

Jmol Dynamic Image

Ammonia Molecule

Log File

Log File

Vibrations and Charges

Display Vibrations

Vibrations, Symmetry & IR Intensity

Mode# Wavenumber (cm-1) Symmetry IR Intensity Image
1 1090 A1 145
2 1640 E 14
3 1694 E 14
4 3461 A1 1
5 3590 E 0
6 3590 E 0

By the 3N-6 rule since N = 4, you should expect 6 vibrational modes.

  Modes 2 and 3 are degenerate; modes 5 and 6 are also degenerate.
  Modes 1,2 and 3 are bending vibrations. Modes 4,5 and 6 are bond stretch vibrations.
  Mode 4 is highly symmetrical
  Mode 1 is the umbrella mode
  To be IR active there needs to a change in dipole moment. You should expect to see 3 but modes 2 and 3 are degenerate so you only see 2 bands.

Atomic Charges

Charge Distribution of the molecule NH3.
Atom Calculated Charge Oxidation State
Nitrogen -1.125 -3
Hydrogen +0.375 +1

You would expect Nitrogen to be negatively charged and Hydrogen to be positively charged. This is because the Nitrogen Atom is more electronegative than the Hydrogen Atom. The computational results agree with the expected charges.

Optimised Structures of N2

N2 Summary

Molecule N2
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -109.52412868 a.u.
RMS Gradient 0.00000060 a.u.
Point Group D∞h
Optimised N-N Bond Length 1.11 Å
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 = -3.400991D-13

Jmol Dynamic Image

Nitrogen Molecule

Log File for Nitrogen

Log File

Vibrations and Charges of Nitrogen

In the image above, the frequency corresponds with the wavenumber in cm-1.

IR Vibrations of the molecule N2.

The molecule is not IR active because it is a homonuclear diatomic so dipoles cancel out, additionally all vibrations for the molecule is symmetrical so not IR active.

Charge Distribution of the molecule N2.

There is no overall charge because the molecule is symmetrical and is a homonuclear diatomic so dipoles cancel out; no overall dipole moment.

Optimised Structures of H2

H2 Summary

Molecule H2
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -1.17853936 a.u.
RMS Gradient 0.00000017 a.u.
Point Group D∞h
Optimised H-H Bond Length 0.74 Å
Item Value Threshold Converged?
Maximum Force 0 0.000450 YES
RMS Force 0 0.000300 YES
Maximum Displacement 0 0.001800 YES
RMS Displacement 0.000001 0.001200 YES

Predicted change in Energy = -1.167770D-13

Jmol Dynamic Image

Hydrogen Molecule

Log File for Hydrogen

Log File

Vibrations and Charges of Hydrogen

IR Vibrations of the molecule H2.

The molecule is not IR active because it is a homonuclear diatomic so dipoles cancel out, additionally all vibrations for the molecule is symmetrical so not IR active.

Charge Distribution of the molecule H2.

There is no overall charge because the molecule is symmetrical and is a homonuclear diatomic so dipoles cancel out; no overall dipole moment.

Mono-metallic TM complex that coordinates N2

Unique Identifier VEJSOV
Link to Structure [Conquest Link ]
N≡N Bond Length 1.116 Å
Publication DOI 10.1002/ejic.201700569
Deposiiton CCDC 1547291


Image of the Transition Metal Complex which coordinates N2.


The experimental bond length is 1.12 Å to 3.s.f whereas the computational is 1.11 Å to 3 s.f.. The small difference in the bond lengths is because the N2 which is coordinated to the metal complex, this bond length is impacted by the other ligands bonded to the metal cation and by the metal cation itself. Bonding to the metal cation via a coordinate bond leads to an elongation of the N2 bond. This is because the transiton metal pulls some of the electron density from the N-N bond towards the N-TM bond therefore, weakening and elongating the N-N bond.

Additionally, the N2 in the metal coordinate is not in the gas phase like the other N2 molecule thus impacting the bond length of the two. However, the difference in bond length is negligible (difference is by 0.01 Å). The computational method used is not that accuarate so there are errors that need to be taken into acccount; a better method needs to be used.

Haber-Bosch Process

The Haber-Bosch process is an industrial process which makes Ammonia from the reactants Hydrogen and Nitrogen. The Ammonia can be used for many other processes i.e. for the use of fertilisers.

E(NH3) -56.55776873 a.u.
2 x E(NH3) -113.11553746 a.u.
E(N2) -109.52412868 a.u.
E(H2) -1.17853936 a.u.
3 x E(H2) -3.53561808 a.u.
ΔE = 2 x(NH3) - [E(N2) + 3 xE(H2)] -0.0557907 a.u. , -146.5 kJ/mol (1 d.p.)
Since the forward reaction is exothermic it means the reaction is thermodynamically feasible so the product, Ammonia, is more stable than the reactants, Nitrogen and Hydrogen.

CO Molecule (Small Molecule)

CO Summary

Molecule CO
Calculation Method RB3LYP
Basis Set 6-31G(d,p)
E(RB3LYP) -113.30945314 a.u.
RMS Gradient 0.00001828 a.u.
Point Group D∞h
Optimised C≡O Bond Length 1.14 Å
Dipole Moment 0.0599


Item Value Threshold Converged?
Maximum Force 0.000032 0.000450 YES
RMS Force 0.000032 0.000300 YES
Maximum Displacement 0.000012 0.001800 YES
RMS Displacement 0.000018 0.001200 YES

Predicted change in Energy = -3.956716D-10

Jmol Dynamic Image

Carbon Monoxide

Log File for Carbon Monoxide

Log File

Vibrations

Vibrational Motion of the molecule Carbon Monoxide

Atomic Charges

Atomic Charge of the molecule Carbon Monoxide


The molecule is linear, but since the Oxygen atom is more electronegative than the Carbon atom that is the reason why the Oxygen atom has a negative atomic charge whereas the Carbon atom has a positive atomic charge.

Mono-metallic TM complex that coordinates CO (Independent Mark)

Unique Identifier HEGMAK
Link to Structure [Conquest Link ]
C≡O Bond Length 1.156 Å
Publication DOI 10.1039/C7DT03096G
Deposition CCDC 1562700
Image of the Transition Metal Complex which coordinates N2.

Molecular Orbitals of Carbon Monoxide

The electronic configuration for -

Carbon: 1s2 2s2 2p2 , Oxygen: 1s2 2s2 2p4

In Carbon Monoxide, Carbon is bonded to Oxygen by a triple bond - this means the bonding is made up of 1 σ bond and 2 π bonds. This means that the the 2s orbitals and 2p orbitals are involved in the bonding for this molecule.

As you can see, looking at MOs 1 and 2, they are very low lying in energy (19.3 a.u. and -10.3 a.u.) this means they are the 2 AOs (1s orbitals of Carbon and Oxygen) and are therefore not involved in the bonding. Additionally, orbitals of the same energy are degenerate.


Atomic Orbital 1s orbital 2s orbital 2p orbital
Molecular Orbital Two 1s orbitals overlapping in phase with eachother Two 2s orbitals overlapping in phase with eachother Two 2p orbitals overlapping in phase with eachother
Type of Bonding Bonding Orbital Bonding Orbital Bonding Orbital
Image
Explanation Since the 1s orbitals are low lying in energy in comparison to the 2s and 2p orbitals, the 1s are not involved in bonding as orbital not available for bonding. This MO is occupied Since the 2s orbital isn't low lying in terms of energy, it is involved in bonding and leads to the formation of the σ bond. No nodes since they two atomic orbitals are in phase with eachother. This MO is occupied. Some p character but negligible. The two 2p orbitals overlap in phase with eachother producing a π bond. Since two 2p orbitals are involved in the bonding these MOs are degenerate in terms of shape and energy. There is a node becuase there is a change in sign in the orbital, it goes from positive to negative which causes the node (an area with zero electron density). This MO is occupied.

Bonding is when there is an interaction between atomic orbitals thus producing a bond whereas the antibonding orbital is the complete opposite as the antibonding orbital doesn't contribute to the bond. Antibonding orbitals contributing to the bond is an unstable and high energy interaction.

HOMO & LUMO Orbitals

HOMO means highest occupied molecular orbital and LUMO means lowest unoccupied molecular orbital. The energies of the HOMO/LUMO are low and are similar to the energies of the bonding 2p and 2s orbitals, they are not high in energy.

Atomic Orbital 2p orbital 2p orbital
Molecular Orbital Two 2p orbitals overlapping out of phase with eachother Two 2p orbitals overlapping out of phase with eachother
Type of Bonding Antibonding Orbital Antibonding Orbital
Image
Explanation From the image above,you can see that the HOMO is an antibonding orbital. This is because there is no overlapping of the same colours in the image. The MO goes from red to blue to red which means it is out of phase so therefore is an antibonding orbital. Looking at the alpha MOs image to the right, it shows that the HOMO (molecular orbital 7) has a similar energy to the other orbitals which suggests that the HOMO is two 2pz atomic orbitals which have overlapped out of phase. This MO is occupied. The LUMO is out of phase and is therefore an antibonding orbital, this is because the 2py orbital has overlap out of phase so there is no interaction between the two atomic orbitals. This means there are nodes since there is no interaction between the two 2py orbitals. This MO is unoccupied.


This is an example of some of the bonding and antibonding molecular orbitals that form when atomic orbtials of CO interact and overlap with eachother.
  • In the image it says a node is change in electron density, that it is a mistake. A node is a region with zero electron density.

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 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 - There is a typo regarding the wavenumber of the 2nd vibration which should be 1694 and not 1640cm-1.

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 0.5/0.5

Have you completed the calculations and included all relevant information? (summary, item table, structural information, jmol image, vibrations and charges)

YES

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 4/5

Have you completed the calculation and included all relevant information?

YES - You could have commented the vibrational mode rather than just stating it.

Have you added information about MOs and charges on atoms?

YES - You commented on the MO energies in general but missed to explain the relative order of the MOs (e.g. looking at the number of nodes). Only the 1s of O is contributing to the first displayed MO. Therefore it is a non-bonding MO and not a bonding one. The HOMO mainly originating from a in-phase overlap of 2pz orbitals and it is a bonding MO. Otherwise two pairs of areas with the same phase would be observed. The shape of the areas is different from what is expected because s orbitals are mixing in.

The comments on the other MOs are correct but for the 2p orbitals you could have been more specific labelling them (2px,2py and 2pz). For bonding and anti-bonding MOs there are interactions between contributing AOs. For bonding MOs these are constructive and the AOs need to be in phase. For anti-bonding MOs the interactions are destructive and the contributing AOs are out-of-phase. Only for non-bonding MOs there are no interactions between the contributing AOs.

Independence 0.5/1

If you have finished everything else and have spare time in the lab you could: Check one of your results against the literature, or

YES - You could have explained differences between experimental and computational bond lengths rather than just stating minimal information.

Do an extra calculation on another small molecule, or Do some deeper analysis on your results so far