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Rep:Mod:THL3318

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NH3 molecule

Summary

Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -56.55776873 au

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 molecule

Optimized N-H bond distance = 1.02Å

Optimized H-N-H bond angle = 106°

Link to the NH3 optimization file can be found here.

Vibrations

'Display Vibrations' window for optimized NH3 molecule.
Wavenumber, Symmetry, and IR Intensity of NH3 Vibrational Modes
Mode Number 1 2 3 4 5 6
wavenumber (cm-1) 1090 1694 1694 3461 3590 3590
symmetry A1 E E A1 E E
intensity (arbitrary units) 145 14 14 1 0 0
image

Questions

  • How many modes do you expect from the 3N-6 rule?
We would expect 6 vibrational modes because there are 4 atoms in NH3, therefore 3(4)-6=6.
  • Which modes are degenerate (ie have the same energy)?
Modes 2,3 and 5,6 are degenerate because they have the same frequency and IR intensity.
  • Which modes are "bending" vibrations and which are "bond stretch" vibrations?
Modes 1,2,3 are bending vibrations (change in angle) while modes 4,5,6 are bond stretch vibrations (change in bond length).
  • Which mode is highly symmetric?
Mode 1 and 4 are highly symmetric.
  • One mode is known as the "umbrella" mode, which one is this?
Mode 1 looks like the opening and closing of an umbrella and would therefore be known as the "umbrella" mode.
  • How many bands would you expect to see in an experimental spectrum of gaseous ammonia?
There are 4 distinct wavenumbers but only 3 have a non-zero intensity, therefore we would expect 3 bands to be present in the experimental spectrum of gaseous ammonia.

Charge Distribution

Charge Distribution of NH3.

Results: Charge Distribution on Hydrogen atom is 0.375 and -1.125 on Nitrogen

Expectation: As expected, the charge distribution on Nitrogen is negative because it is more elctronegative than hydrogen thus drawing electrons closer to the Nitrogen atom.

N2 molecule

Summary

Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -109.52412868 au

Point Group: D∞h 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000006     0.000450     YES
 RMS     Force            0.000006     0.000300     YES
 Maximum Displacement     0.000002     0.001800     YES
 RMS     Displacement     0.000003     0.001200     YES
N2 molecule

Optimized N-N bond distance = 1.11Å

Link to the N2 optimization file can be found here.

Vibrations

'Display Vibrations' window for optimized N2 molecule.
Wavenumber, Symmetry, and IR Intensity of N2 Vibrational Modes
wavenumber cm-1 2457
symmetry SGG
intensity arbitrary units 0
image

Charge Distribution

Charge Distribution of N2.

Results: Charge Distribution on Nitrogen atom is 0.0

Expectation: As expected, the charge distribution on Nitrogen is 0 because the electronegativity of both Nitrogen atoms are equal with result in equal sharing of electron density between the two atoms.

H2 molecule

Summary

Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -1.17853930 au

Point Group: D∞h 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000211     0.000450     YES
 RMS     Force            0.000211     0.000300     YES
 Maximum Displacement     0.000278     0.001800     YES
 RMS     Displacement     0.000393     0.001200     YES
H2 molecule

Link to the H2 optimization file can be found here.

Optimized H-H bond distance = 0.74Å

Vibrations

'Display Vibrations' window for optimized H2 molecule.
Wavenumber, Symmetry, and IR Intensity of N2 Vibrational Modes
wavenumber cm-1 4461
symmetry SGG
intensity arbitrary units 0
image

Charge Distribution

Charge Distribution of NH3.

Results: Charge Distribution on Hydrogen atom is 0.0

Expectation: As expected, the charge distribution on Hydrogen is 0 because the electronegativity of both Hydrogen atoms are equal with result in equal electron density surrounding the atoms.

Mono-metallic TM complex that coordinates N2

Structure of WUQSEH: (2,6-bis((bis(2,4,6-tris(trifluoromethyl)phenyl)phosphino)oxy)phenyl)-(dinitrogen)iridium toluene solvate.

CDC of WUQSEH can be found here: [1]

N-N bond length: 1.11Å

The N-N bond length in the crystal structure is equal to the N-N bond length found in an N2 molecule. Using MO theory, we can know that adding electron density to the N-N triple bond would fill up the anti-bonding orbitals. This would result in a decrease in bond length caused by a decrease in bond order as anti-bonding orbitals are filled. In the mono-metallic TM complex shown above, the TM Ir is bonded to 4 substituents, namely a phenyl group, two P atoms bonded to O, and the N-N group. The phenyl group is a very good electron drawing group due to its ring currents. P on the other hand has a very similar electronegativity to Ir. We can therefore presume that the electron density surround the central TM has been mainly shifted towards the phenyl group rather than the N-N group even though N has a higher electronegativity than Ir. As a result the N-N bond length remains unchanged due to no change in electron density

Haber-Bosch process

  • E(NH3)= -56.5577687 au
  • 2*E(NH3)= -113.1155375 au
  • E(N2)= -109.5241287 au
  • E(H2)= -1.1785393 au
  • 3*E(H2)= -3.5356179 au
  • ΔE=2*E(NH3)-[E(N2)+3*E(H2)]= -0.0557909 au = -146.5 KJ/mol (to 1 dp)

The energy for converting hydrogen and nitrogen gas into ammonia gas is -146.5 KJ/mol. Therefore the ammonia product is more stable than the gaseous reactants because it is lower in energy and the overall reaction is exothermic.

Project Molecule (ClF5)

Summary

Calculation Method: RB3LYP

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

Final energy E(RB3LYP) in au: -958.98366404

Point Group: C4V 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000075     0.000450     YES
 RMS     Force            0.000018     0.000300     YES
 Maximum Displacement     0.000231     0.001800     YES
 RMS     Displacement     0.000080     0.001200     YES
ClF5 molecule

Optimized Cl-F(axial) bond distance = 1.65Å

Optimized Cl-F(equatorial) bond distance = 1.70Å

Optimized F(axial)-Cl-F(equatorial) bond angle = 86°

Optimized F(equatorial)-Cl-F(equatorial) bond angle = 90°

Link to the ClF5 optimization file can be found here.

'Display Vibrations' window for optimized ClF5 molecule.
Wavenumber, Symmetry, and IR Intensity of ClF5 Vibrational Modes
Mode Number 1 2 3 4 5 6
wavenumber cm-1 259 280 280 347 452 452
symmetry B2 E E B1 E E
intensity arbitrary units 0 0 0 0 0 0
image
Mode Number 7 8 9 10 11 12
wavenumber cm-1 471 521 560 734 804 804
symmetry A1 B2 A1 A1 E E
intensity arbitrary units 28 0 7 75 404 404
image

Charge Distribution

Charge Distribution of ClF5.

Results: Charge Distribution on Chlorine is 1.998 and -0.335 on Fluorine. Expectation: As expected, the charge distribution on Fluorine is more negative because it is more elctronegative than Chlorine thus drawing electrons closer to the Fluorine atoms.

Molecular Orbitals

Wavenumber, Symmetry, and IR Intensity of ClF5 Vibrational Modes
Image
AOs which contribute to the MOs Cl 2s, F 2s F 2p Cl 3p, F(equatorial) 2p, F(axial) 2s Cl 3p, F 2p Cl 3d, F 2p
Bonding, anti-bonding, or mixture? Bonding Anti-bonding Anti-bonding Anti-bonding Anti-bonding
Deep in energy, in the HOMO/LUMO region, or high in energy? Deep in energy Deep in energy HOMO LUMO High in energy
Occupied or unoccupied Occupied Occupied Occupied Unoccupied Unoccupied
Effect of MO on bonding Strengthens bonding if occupied Weakens bonding if occupied Weakens bonding if occupied Weakens bonding if occupied Weakens bonding if occupied

(Independence) H2O2 molecule

Summary

Calculation Method: RB3LYP

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

Final energy E(RB3LYP): -151.54319138 au

Point Group: C2 

         Item               Value     Threshold  Converged?
 Maximum Force            0.000075     0.000450     YES
 RMS     Force            0.000038     0.000300     YES
 Maximum Displacement     0.000349     0.001800     YES
 RMS     Displacement     0.000381     0.001200     YES
H2O2 molecule

Optimized O-O bond distance = 1.46Å

Optimized O-H bond distance = 0.97Å

Optimized H-O-O bond angle = 100°

Link to the H2O2 optimization file can be found here.

Vibrations

'Display Vibrations' window for optimized H2O2 molecule.
Wavenumber, Symmetry, and IR Intensity of H2O2 Vibrational Modes
Mode Number 1 2 3 4 5 6
wavenumber (cm-1) 342 955 1311 1447 3762 3763
symmetry A A B A A B
intensity (arbitrary units) 198 2 110 0 6 33
image

Charge Distribution

Charge Distribution of H2O2.

Results: Charge Distribution on Hydrogen atoms is 0.478 and -0.478 on the Oxygen atoms.

Expectation: As expected, the charge distribution on Oxygen more negative than that on Hydrogen because the electronegativity of Oxygen is greater thus resulting in the electron density being around oxygen more than hydrogen.

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

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 - mode 4 is too low in energy as well to be detected in an experimental spectrum, so only 2 bands will be seen.

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

Have you added information about MOs and charges on atoms?

YES

You could have analysed the calculated vibrations as you did for NH3.]You correctly identified contributing AOs. The second displayed MOs is rather non-bonding if only the 22p orbital is considered to participate. When taking small contributions of the the F s orbitals into account this orbital could be described as a bonding one. You haven't stated the number of the last MO, so it cannot be identified and therefore not checked if your analysis is correct. I compared all MOs up to number 50 with yours and couldn't figure out which one it is. You could have explained and analysed the relative energies of the MOs in more detail.

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

YES

Do some deeper analysis on your results so far

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