Rep:Mod:st6218
Chemistry
NH3
Optimization Results Summary
Molecule: NH3
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
Final Energy E(RB3LYP): -56.55776873 a.u.
RMS Gradient: 0.00000323 a.u.
Point Group: C3V
Item Value Threshold Converged? Maximum Force 0.000006 0.000450 YES RMS Force 0.000004 0.000300 YES Maximum Displacement 0.000014 0.001800 YES RMS Displacement 0.000009 0.001200 YES
NH3 |
Optimised N-H Bond Distance: 1.02Å
Optimised H-N-H Bond Angle: 106°
The optimisation file is linked here
Vibrations
| Information | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| |||||||||||||||||
| wavenumber/ cm-1 | symmetry | intensity/a.u. | wavenumber/ cm-1 | symmetry | intensity/a.u. | wavenumber/ cm-1 | symmetry | intensity/a.u. | wavenumber/ cm-1 | symmetry | intensity/a.u. | wavenumber/ cm-1 | symmetry | intensity/a.u. | wavenumber/ cm-1 | symmetry | intensity/a.u. |
| 1090 | A1 | 145 | 1694 | E | 14 | 1694 | E | 14 | 3461 | A1 | 1 | 3590 | E | 0 | 3590 | E | 0 |
how many modes do you expect from the 3N-6 rule? Answer: 6
which modes are degenerate (ie have the same energy)? Answer: The modes at 1694 cm-1 and 3590 cm-1.
which modes are "bending" vibrations and which are "bond stretch" vibrations? Answer: bend-1090 and 1694 cm-1 stretch-3461 and 3590 cm-1.
which mode is highly symmetric? Answer: stretch with wavenumber of 3461 cm-1.
one mode is known as the "umbrella" mode, which one is this? Answer: bend with wavenumber of 1090 cm-1.
how many bands would you expect to see in an experimental spectrum of gaseous ammonia? Answer: I expect to see at least 3 bands at low temperature.
Charge Analysis
Charge of N in NH3 = -1.125 Charge of H in NH3 = +0.375
The charges are expected as N is more electronegative than H and hence it will draw the electron density away from H, causing it to be more negatively charged since electrons are negative charges.
N2
Optimization Results Summary
Molecule: N2
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: 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
N2 |
Optimised N-N Bond Distance: 1.11 Å
The optimisation file is linked here
Vibration
| Information | ||
|---|---|---|
| ||
| More Info | ||
| wavelength/cm-1 | symmetry | intensity/a.u. |
| 2457 | SGG | 0 |
Charge Analysis
Charge of N in N2 = 0
This is expected as N2 is made up of the same atoms and hence no dipole moment between the two atoms. This meant that they have to share the electron density evenly, leading to zero charge on either atoms.
Bond length comparison
The bond length of N2 is 1.12 Å and 1.13 Å in the structure of AFUXAD (https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=AFUXAD&DatabaseToSearch=Published)
The bond length is longer than the one in just N2 because when the bond is formed, the electrons from the non-bonding d orbital of the transition metal is added to the lowest unoccupied molecular orbital of N2, which is an anti-bonding orbital (π*). This results in a lowering of the bond order and hence the bond between N-N is weakened and is reflected in the longer bond length in the structure of AFUXAD.
H2
Optimization Results Summary
Molecule: H2
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
Final Energy E(RB3LYP): -1.17853936 a.u.
RMS Gradient: 0.00000017 a.u.
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
H2 |
Optimised H-H Bond Distance: 0.74 Å
The optimisation file is linked here
Vibration
| Information | ||
|---|---|---|
| ||
| More Info | ||
| wavelength/cm-1 | symmetry | intensity/a.u. |
| 4466 | SGG | 0 |
Charge Analysis
Charge of H in H2 = 0
This is expected as H2 is made up of the same atoms and hence no dipole moment between the two atoms. This meant that they have to share the electron density evenly, leading to zero charge on either atoms.
Haber-Borsh Process
N2 + 3H2 → 2NH3
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)] = -0.0557907 a.u.
since 0.000038 a.u. = 0.1 kJ/mol
-0.0557907 a.u. = 146.8 kJ/mol
CO
Optimization Results Summary
Molecule: N2
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
Final Energy E(RB3LYP): -113.30945314 a.u.
RMS Gradient: 0.00000433 a.u.
Point Group: C*V
Item Value Threshold Converged? Maximum Force 0.000007 0.000450 YES RMS Force 0.000007 0.000300 YES Maximum Displacement 0.000003 0.001800 YES RMS Displacement 0.000004 0.001200 YES
CO |
Optimised C-O Bond Distance: 1.14 Å
The optimisation file is linked here
Vibration
| Information | ||
|---|---|---|
| ||
| More Info | ||
| wavelength/cm-1 | symmetry | intensity/a.u. |
| 2209 | SG | 68.0 |
Charge Analysis
Charge of C in CO = +0.506 Charge of O in CO = -0.506
This is expected as O is more electronegative than C and hence negatively charged electron density will be drawn to O, resulting in the above observation.
Bond length comparison
The bond length of CO is 1.15 Å in the structure of ACAVOS (https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=acavos&DatabaseToSearch=Published)
The bond length is longer than the one in just CO because when the bond is formed, the electrons from the non-bonding d orbital of the transition metal is added to the lowest unoccupied molecular orbital of CO, which is an anti-bonding orbital (π*). This results in a lowering of the bond order and hence the bond between CO is weakened and is reflected in the longer bond length in the structure of ACAVOS.
Additionally, the literature value of the CO bond is 1.13 Å[1] , which is in good agreement with our bond length. The difference in length could be resulted by different value of equilibrium position taken.
Molecular Orbital
| Molecular Orbital | Description |
|---|---|
 |
2s orbitals from C and O contributed to this bonding MO which is fully occupied. This is deep in energy (-1.16 a.u.) as s orbitals penetrate deep into the core electron shells, stabilising the orbital. The electron density leans towards O as O has a greater contribution to the bonding MO ( it's orbital is closer in energy level to the bonding MO). |
 |
2s orbitals from C and O contributed to this anti-bonding MO from destructive interference. This orbital is fully occupied.The electron density leans towards C as C has a greater contribution to the anti-bonding MO. This is because the 2s orbital from C is higher in energy than O as it has a lower atomic number but similar core shielding. This makes the energy level of C's 2s orbital closer to the anti-bonding 2s orbital, allowing greater contribution, reflected by the skew in electron density towards C. |
 |
2p orbitals from C and O contribute to this bonding MO from constructive inference. This orbital is fully occupied and is the Highest Occupied Molecular Orbital (HOMO) with an energy level of -0.37 a.u. and hence likely to react well with Lowest Unoccupied Molecular Orbital (LUMO) of other molecules with similar energy level. The electron density is again skewed towards O as it has a greater contribution to this bonding MO. |
 |
2p orbitals from C and O contribute to this anti-bonding MO from destructive inference. This orbital is unoccupied and is the Lowest Unoccupied Molecular Orbital (LUMO) of the molecule with an energy level of -0.0218 a.u. and has another degenerate orbital perpendicular to this orbital. Addition of electron density into this orbital will lower the overall bond order of the bond. |
 |
This orbital has a lower energy than the sigma orbital due to mixing (factors such as a good aligned overlap helps to improve mixing), which given more s character, have more penetration and thus a lower energy. |
References
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 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 - You correctly stated two sets of degenerate vibrations. This explains a spectrum with 4 bands. All stretching vibrations are too low in intensity too be observed in an experimental spectrum. A spectrum with only 2 bands is expected.
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 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 your results.
Your choice of small molecule 4/5
Have you completed the calculation and included all relevant information?
YES
Have you added information about MOs and charges on atoms?
YES
You missed analyse the 5th displayed MO in more detail. You could have explained the energetic order of the displayed MOs.
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
YES
Do an extra calculation on another small molecule, or
Do some deeper analysis on your results so far