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Year 2 Computational Lab Sam Young

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BH3 Molecule

Basis set

6-31G(d,p)

Summary

Item Table

    Item               Value     Threshold  Converged?
 Maximum Force            0.000003     0.000450     YES
 RMS     Force            0.000002     0.000300     YES
 Maximum Displacement     0.000013     0.001800     YES
 RMS     Displacement     0.000006     0.001200     YES
 Predicted change in Energy=-6.245437D-11
 Optimization completed.
    -- Stationary point found. 

Link to file

Media:SLY_BH3_FREQ.log

Frequency Table

 Full mass-weighted force constant matrix:
 Low frequencies ---   -0.8713   -0.6455   -0.0055    8.0386   12.6754   12.7053
 Low frequencies --- 1157.7354 1205.3451 1205.3474

Jmol Image

Optimised BH3 Molecule

Vibrational Spectrum of BH3

wavenumber (cm-1 Intensity (arbitrary units) symmetry IR active? type
1157 94 A2" yes out-of-plane bend
1205 14 E' slight bend
1205 14 E' slight bend
2576 0 A1' no symmetric stretch
2704 143 E' yes asymmetric stretch
2704 143 E' yes asymmetric stretch

There are fewer than 6 peaks present in the IR spectrum despite there being 6 vibrational modes, due to one mode not being IR active, and two pairs of degenerate vibrational modes.

MO Diagram

The qualitative approach provides a simple yet similar image to the computer generated MOs, and in this particular example there are no significant differences between the two. However, when going onto larger molecules, qualitative MOs which get more complicated are often simplified, therefore computer generated MOs are more useful for larger molecules.

Reference: http://www.huntresearchgroup.org.uk/teaching/teaching_comp_lab_year2a/Tut_MO_diagram_BH3.pdf

NH3 Molecule

Basis Set

6-31G(d,p)

Summary

Item

Item               Value     Threshold  Converged?
 Maximum Force            0.000110     0.000450     YES
 RMS     Force            0.000039     0.000300     YES
 Maximum Displacement     0.000631     0.001800     YES
 RMS     Displacement     0.000225     0.001200     YES
 Predicted change in Energy=-3.946669D-08
 Optimization completed.
    -- Stationary point found.

Link to file

Media:SLYNH3_FREQ.log

Frequency Table

Full mass-weighted force constant matrix:
 Low frequencies ---   -0.2194   -0.1785   -0.0058   20.6664   20.6917   30.8835
 Low frequencies --- 1000.9070 1673.7928 1673.7929

Jmol Image

Optimised NH3 Molecule

NH3BH3 Molecule

Basis Set

6-31G(d,p)

Summary

Item

      Item               Value     Threshold  Converged?
 Maximum Force            0.000243     0.000450     YES
 RMS     Force            0.000054     0.000300     YES
 Maximum Displacement     0.001390     0.001800     YES
 RMS     Displacement     0.000382     0.001200     YES
 Predicted change in Energy=-1.938548D-07
 Optimization completed.
    -- Stationary point found.

Link to file

Media:NBH6FREQSAM.log

Frequency Table

Full mass-weighted force constant matrix:
 Low frequencies ---   -0.1897   -0.0663   -0.0074    9.9186   16.5521   16.5669
 Low frequencies ---  263.0129  631.3811  638.8655

Jmol Image

Optimised NH3BH3 Molecule

Energies

E(BH3) = -26.61722 a.u.

E(NH3) = -56.56699 a.u.

E(BH3NH3) = -83.22469 a.u.

ΔE=[E(NH3)+E(BH3)] - E(NH3BH3) = 0.04048 a.u.

ΔE = 0.04048/0.0004 = 101 KJ/mol

As a point of comparison the C-N bond has a bond dissociation energy of -290 KJ/mol, suggesting that the value we have calculated for the B-N bond is low, therefore a weaker bond.


Reference: https://opentextbc.ca/chemistry/chapter/7-5-strengths-of-ionic-and-covalent-bonds/

Ethane & BH3NH3

Charge Distribution of Ethane

Charge Distribution of BH3NH3

We can clearly see that the C-C Bond for ethane is non polarised due to it being a completely symmetric bond, while the N-B bond is highly polarised, with electron density towards the N, due to a fairly large electronegativity difference between the two atoms. It is possible to chemically manipulate the charges on the bonds by adding an electronegative substituent, for example, an alcohol group.

Charge Distribution of Ethanol

Here the charge distribution along the C-C bond has been altered due to the electronegative oxygen group being added. Now the C bonded to the O has a less negative value due to O drawing electorn density towards itself.

BBr3

DOI:10042/202310

Basis Set

GEN


Summary

Item

Item               Value     Threshold  Converged?
 Maximum Force            0.000008     0.000450     YES
 RMS     Force            0.000005     0.000300     YES
 Maximum Displacement     0.000036     0.001800     YES
 RMS     Displacement     0.000023     0.001200     YES
 Predicted change in Energy=-4.027373D-10
 Optimization completed.
    -- Stationary point found.     

Link to file

Media:BBr3FreqSam.log

Frequency Table

 Full mass-weighted force constant matrix:
 Low frequencies ---   -0.0137   -0.0064   -0.0047    2.4315    2.4315    4.8421
 Low frequencies ---  155.9631  155.9651  267.7052

Jmol Image

Optimised BBr3 Molecule

Aromaticity Mini Project

Benzene

Basis set

6-31G(d,p)

Summary

Item

 Item               Value     Threshold  Converged?
 Maximum Force            0.000193     0.000450     YES
 RMS     Force            0.000079     0.000300     YES
 Maximum Displacement     0.000830     0.001800     YES
 RMS     Displacement     0.000294     0.001200     YES
 Predicted change in Energy=-4.437691D-07
 Optimization completed.
    -- Stationary point found. 

Link to file

Media:BENFREQSAM.log

Frequency Table

 Full mass-weighted force constant matrix:
 Low frequencies ---   -3.5606   -3.5606   -0.0088   -0.0040   -0.0040   10.0905
 Low frequencies ---  413.9582  413.9582  621.1416

Jmol Image

Optimised Benzene Molecule

Borazine

Basis Set

6-31G(d,p)


Summary

Item

 Item               Value     Threshold  Converged?
 Maximum Force            0.000081     0.000450     YES
 RMS     Force            0.000031     0.000300     YES
 Maximum Displacement     0.000238     0.001800     YES
 RMS     Displacement     0.000071     0.001200     YES
 Predicted change in Energy=-8.399586D-08
 Optimization completed.
    -- Stationary point found. 

Link to file

Media:BorazineFreqSam.log

Frequency Table

 
 Full mass-weighted force constant matrix:
 Low frequencies ---   -6.6262   -6.4470   -5.9957   -0.0097    0.0573    0.1401
 Low frequencies ---  289.2549  289.2653  403.8557

Jmol Image

Optimised Borazine Molecule

Charge Distribution

Charge distribution of Benzene

Charge distribution of Borazine


Atom Charge distribution Discuss
Benzene - C -0.239 All carbon atoms in benzene are identical in terms of charge distributrion due to them all being in the same chemical environments. Negative value as they are more electronegative than the hydrogen atoms, therefore attract electron density. (C = 2.55, H = 2.20)
Benzene - H 0.239 All Hydrogen atoms in benzene are also identical therefore all have equal charge density. Positive value as they are more electropositive than Carbon so electron density is pulled away from them. (C = 2.55, H = 2.20)
Borazine - N -1.102 Negative value due to high electronegativity of Nitrogen, attracting electron density towards itself. (N = 3.04)
Borazine - B .0747 Positive value due to boron being the most electropositive atom in the ring, therefore attracting the least electron density. (B = 2.04)
Borazine - H-(N) 0.432 Slightly positive value due to electronegativity difference of H and the directly attatched N atom which draws electron density away from the proton. (H = 2.20, N = 3.04)
Borazine - H-(B) -0.077 Slightly negative due to H being more electronegative than B, therefore it draws electron density towards itself. (B = 2.04, H = 2.20)

The main difference between the charge distribution of Benzene and Borazine, is that benzene is highly symmetric so all C atoms have the same charge density, as do all H atoms. However, due to the alternating N and B atoms in the Borazine ring, the charge distribution causes the H atoms to have different charge densities depending on whether they're bonded to N or B.

Reference for values : https://sciencenotes.org/list-of-electronegativity-values-of-the-elements/

Molecular Orbital Comparison

MO (Benzene) Image MO (Borazine) Image Comparison
MO8 MO8 The MO8 of Benzene is highly symmetric across the molecule, with one node running down the middle and contributions from all atoms except two of the Hydrogen aotms. MO8 of Borazine resembles the MO of benzene in that it has one node, however, it is less symmetric and has no contribution from 4 Hydrogen atoms and from one Nitrogen atom.
MO14 MO15 MO14 of Benzene and MO15 of Borazine are practically identical and display the sigma framework of the ring with 3 nodes.
MO21 MO21 MO21 of both Benzene and Borazine are also very similar, showing contributions from the orthogonal pz orbitals, although that of Borazine is less symmetric with one lobe being more curved than the other. This is one of the degenerate pairs of HOMO orbitals of both molecules. It shows a node perpendicular to the plane of the molecule with favorable pi-electron interations either side .

Ng611 (talk) 23:03, 15 May 2018 (BST) Comparison of the orbitals is correct but some more detail in this section would have been useful. Why are there differences between the benzene/borazine MOs? Which orbitals give rise to the MO's and what is its symmetry?

Concepts of Aromaticity

Aromaticity refers to the additional stabilisatoin of certain molecules, as a result of resonance energy caused by an orthogonal cyclic array of p-orbitals. Furthermore, there are a set of requirements a molecule must fulfill in its ground state in order to be considered as aromatic; i) They must be cyclic with bonds of equal lengths. ii) They must obey Huckels Law i.e. The molecule must have (4n+2) pi electrons in a continuous ring of p-orbitals adjacent to the molecule. (Where n = 0 or n = a positive integer). Although they often are planar molecules, this is not required for aromaticity.

Ng611 (talk) 23:05, 15 May 2018 (BST) What are some of the other phenomena that give rise to aromaticity in non planar molecules?

As well as the extra stabilization gained, one can identify aromaticity by proton-NMR analysis, as in an applied magnetic field, the pi electron ring is induced causing the protons on the outside of the ring to be deshielded, therefore are found downfield, and the reverse would theoretically apply for internal ring protons. (e.g. Benzene gives a singlet at 7.27ppm). Moreover, the concept of antiaromaticity applies for molecules with the same requirements as above, however on require (4n) pi-electrons, and this gives an overall destabilisation, although moleucules often to adopt different conformations to avoid this. Also, sigma aromaticity exists for inorganic saturated rings, whereby these rings display similar characteristics and behavior to pi-aromatic rings.

Ng611 (talk) 23:05, 15 May 2018 (BST) Excellent paragraph!

In comparing the real MOs of Benzene to the common concept of aromaticity, it appears as though it is only MO17 which displays the idea of the continuous ring of orthogonal p-orbitals, therefore the real picture suggests that the sigma framework and other pi-bonding orbitals play an important role in the stabilization of aromatic molecule. Due to the fact that the traditional idea of the aromatic ring only contributes to 1 of the 14 filled valence MOs, it can be said that this is a very basic concept and the stabilisation is due to a variety of MOs rather than just the one.

Ng611 (talk) 23:05, 15 May 2018 (BST) True. The nature of aromaticity has been considered by other scientists extensively. Discussing their conclusions would have strengthened this final paragraph significantly.

Ng611 (talk) 23:07, 15 May 2018 (BST) A good report overall. Your MO analysis was good, but your MOs for the 2 highest energy antibonding orbitals were incorrect. The section on aromaticity was generally good - remember to use the same colour scale when comparing charge distributions. Your section on benzene/borazine MO analysis was also good - a rationalisation of the differences between the orbitals would have improved this further, as would a more sophisticated discussion of the contemporary view of aromaticity.

MO17


Reference : https://onlinelibrary.wiley.com/doi/epdf/10.1002/chem.200700250 Reference : https://www.ncbi.nlm.nih.gov/pubmed/16839038