Rep:Mod:01496292
NH3 molecule
Summary
N-H bond distance = 1.02 Å
H-N-H bond angle = 106°
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
Final Energy E(RB3LYP): -56.55776873 a.u.
RMS gradient: 0.00000485 a.u.
Point Group: C3V
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
NH3 |
The optimisation file is liked to here
Screenshot of the "Display Vibrations"
how many modes do you expect from the 3N-6 rule?
6.
which modes are degenerate (ie have the same energy)?
Vibration 2,3 and vibration 5,6.
which modes are "bending" vibrations and which are "bond stretch" vibrations?
Mode 1,2,3 are bending. Mode 4,5,6 are bond stretch.
which mode is highly symmetric?
Mode 1,4 is highly symmetric
one mode is known as the "umbrella" mode, which one is this?
Mode 1.
how many bands would you expect to see in an experimental spectrum of gaseous ammonia?
We expect to see 4 bands but only two peak can be observed because mode 2,3 and 5,6 are degenerate.
Atomic Charges
The charge on the N-atom is -1.125 and that on the H-atom is 0.375. The negative charge is expected to be on the N-atom due to its higher electronegativity.
H2 molecule
Summary
H-H bond distance = 0.74 Å
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
Linear strucure
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
The optimisation file is liked to here
H2 |
Screenshot of the "Display Vibrations"
| Mode | Frequency | Intensity |
|---|---|---|
| 1 | 4465.68 | 0.0000 |
NBO charge
The NBO charge on both hydrogens is 0 due to its symmetry.
N2 molecule
Summary
N-N bond distance = 1.11 Å.
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
Linear strucure
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
The optimisation file is liked to here
N2 |
Screenshot of the "Display Vibrations"
| Mode | Frequency | Intensity |
|---|---|---|
| 1 | 2457.33 | 0.0000 |
NBO charge
The NBO charge on both Nitrogens is 0.
Mono-metallic TM complex coordinates H2
DENQET https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=denqet&DatabaseToSearch=Published
H-H bond length = 1.14 Å
The computational data are different from the experimental data because the software has set parameters whilst the experimental data is acquired in different environments which may affect the experimental results.
From the MO perspective, electron on the H-H is promoted to the antibonding orbital from the bonding orbital when it bonds to the central metal so that its bond order is reduced, hence we expect an increase in the bond length.
The Gaussian also has a finite data-base and fixed algorthm is applied. The H-H in TM complex has longer bondlength because it is weaker. When both H's form bond with the TM, the TM pulls electron density from the H-H bond to form TM-H bond. Whereas for H2 the bond density is not changed , so it is shorter and stronger.
E(NH3)= -56.55776873 2*E(NH3)= -113.1155375 E(N2)= -109.52412868 E(H2)= -1.17853936 3*E(H2)=-3.53561808 ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.05579074 a.u. =-146.5 kJ/mol
The ammonia product is more stable.
Cl2 small molecule
Summary
Cl-Cl bond distance = 2.04 Å
Calculation Method: RB3LYP
Basis Set: 6-31G(d,p)
Final Energy E(RB3LYP): -920.34987886 a.u.
RMS gradient: 0.00002510 a.u.
Point Group: D∞h
Linear strucure
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
The optimisation file is liked to here
Cl2 |
Screenshot of the "Display Vibrations"
| Mode | Frequency | Intensity |
|---|---|---|
| 1 | 520.32 | 0.0000 |
The Cl2 molecule has one stretch vibration mode only and because the stretch is symmetrical, there isn't any change in the dipole moment, hence not active on the IR-spectrum.
NBO charge
The NBO charge on both chlorines is 0 due to its symmetry.
Screenshot of MOs
1. 
2. 
3. 
4. 
5. 
Diagram 1. dipicts an overlap of two 3s AOs. This overlap of the two occupied AOs develops a bonding MO because they are in the same phase. As a consequence, the energy will drop and the bonding will be strengthened. This MO bonding is a sigma bonding MO.
Diagran 2. dipicts a side-on overlap of two 2pz AOs. These two occupied antiphase AOs lead to a decrease in bond order so the bonding will be weakened. This MO bonding is a sigma star anti-bonding MO.
Diagram 3. dipicts an side-on overlap of two 2pz AOs as well but conversely this MO is formed by the overlap of two in-phase 2pz AOs. As a result, the bond is strengthened by the sigma bonding MO.
Diagram 4. dipicts an head-on overlap of two 3px or 3py AOs. The symmetry of these two AOs causes an destructive effect on the bonding as in the bond order will decrease. This bonding is a pi-star antibonding MO.
Diagram 5. dipicts an overlap of two 3pz AOs. The anti-phase overlap of them increases the overall energy of the MO. This bonding is a sigma-star antibonding MO.
Diagram 3. and 5. are same MO bondings, but because the 3. is lower in energy and also 2pz is smaller than 3pz, the increase in energy of 3pz is significantly lower. This explain why 3. is deeper in energy than 5.
Diagram 1, 2, 3 are formed by AOs which are deeper in energy (principle quantum shell number smaller than that of HOMO), so the overlap is weak (poor overlap can also be observed from the MO diagrams).
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 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 - except for the part on the Haber-Bosch which appears without a heading within the comparison to the crystal structure.
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, however you did miss out explaining exactly why only 2 modes are seen in the vibrational section. You correctly stated that there are two sets of degenerate modes - this explains a spectrum with 4 peaks. However there are only 2 peaks visible as peaks 4, 5 and 6 are of too low an intensity to be visible.
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, you could have explained that the charges are 0 as the electronegativities are equal and why the intensities of the calculated vibrations are 0.
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?
You should have used between 5 and 7 decimal places for the energy given in Hartree. One decimal place for the energy in kJ/mol is correct.
Have you answered the question, Identify which is more stable the gaseous reactants or the ammonia product?
YES
Your choice of small molecule 3.5/5
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 could have explained the charges using an electronegativity argument instead of stating symmetry to be the reason. Your comments on the MOs 1, 4 and 5 are correct. MOs 2 and 3 are neither bonding nor anti-bonding. They are non-bonding as the AOs of the Cl atoms do not interact at all. Therefore, your conclusion of the effect of MO 2 and 3 regarding the influence on bonding are incorrect!
Independence 0/1
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
NO - no independent work can be identified