Talk:Mod:gjsmodule1

FEEDBACK

Q1: Your energy values are all correct although there is no need to report so many significant figures – there is some error to account for given that this is an approximation and the values won’t be the same beyond a certain point if the calculation is repeated from scratch. The exo- and endo- dimers are not conformational isomers – they are diastereoisomers. The main difference between the strain between the monohydrogenated compounds is correctly identified as bending-strain and well explained. The discussion of kinetic vs thermodynamic control is spot on: you correctly point out that it is not possible to comment on the outcome of the hydrogenation without more information. Most hydrogenation conditions involve a metal catalyst and gaseous hydrogen, are irreversible, and therefore under kinetic control. Modelling with DFT methods would allow calculation of transition state energies and therefore prediction of the kinetic product.

Q2. Your calculated values for compound 10 are good but the lowest energy structure for 9 is too low; in fact 9 should be the higher energy isomer – as you found with the different molecular mechanics force field. It would have been beneficial to see some jmol structures to see why this is the case. 6-ring conformations are a logical focus for optimisation because there are known preferences to analyse – some addition discussion of other ways in which you optimised the compounds would have been good. Hyperstable alkenes are correctly defined.

Q3. The calculations, MOs and IR stretches look good. You should make sure you report all of the energies you calculate in future modules – as these numbers are one of the ways the reports are assessed and without other results as in this question it would be difficult to work out whether the calculations are correct. The discussions of double bond nucleophilicity and the pi-sigma* interaction are good and the IR stretch differences are rationalised well.

Q4. Your assessment of A/B/C/D vs A*/B*/C*/D* is correct with the former group all being lower in energy. The energies you got are a little high, there are lower energy conformations accessible to some of your isomers, in particular when the carbonyl oxygen of the acetyl group is moved closer to the oxonium carbon. Also some of your * structures are not conformations in which the orientation of the acetyl carbonyl oxygen has switched. The combination of R=methyl and semi-empirical calculations is the correct choice for this question. You should have found that using PM6, A=C and B=D; the neighbouring group effect is directly incorporated into the structure which is a non-classical carbocation. Selectivity in the reaction is due to a combination of favoured formation of A/B/C/D over A*/B*/C*/D* and also higher reactivity of A and B due to more favourable orientation for attack on the oxonium group. This is reflected in your finding that C* and D* are much higher in energy, precluding reaction via these pathways.

MP. The comparison of the lit data for isomer A with the calculated data for A, B, C, and D is an interesting question for a mini-project and is exactly the type of scenario where this kind of NMR calculation is applied in computational research. It seems that it is difficult to distinguish these isomers by calculating NMR data – if the actual data are very close it will be impossible no matter how accurate the methods and calculations. Your analysis would have benefited from some kind of analysis of the error between the calculated and lit values. A graphical representation of the ppm differences is often the best way to do this, but more sophisticated statistical analyses are possible. As you have found, the calculated IR data does not seem to be accurate enough for this kind of investigation. The differences in energy you found for these isomers are not insignificant: In conformational analysis, a difference in energy of around 2 kcal/mol will correspond to a >9:1 preference for the lower energy for the lower energy isomer at room temperature. It is typical for comparison of energies to set one isomer at 0 and then give the other values relative to this standard.