Talk:Mod:Pterodactyladiene

Q1: Your energy values are spot on and the discussion of strain contributions is good. It is not necessary to give so many decimal places in the results because these are approximations with some degree of error. You are right that the discussion of thermodynamic vs kinetic control can only be limited: The dimerization must be under kinetic control because the lowest energy molecule is not formed. The hydrogenation will give molecule 4 if the reaction is under thermodynamic control, but under other conditions information about the mechanism and transition state calculations will be needed.

Q2. While atropisomerism is often exhibited in cases where there is restricted rotation of aromatic rings (e.g. BINOL), this is not the case here – there are no aromatic rings! It is just a case of restricted rotation in a different sense (it is difficult for the carbonyl group to flip its orientation because the barrier to rotation is high). Your energies and structures are good, but it would have been nice to see some discussion about how you came to these results – e.g. showing some higher energy conformations that you found and looking at what was the key structural feature to change. The definition of a hyperstable alkene is correct – calculation of the olefin strain is a good extra although it would be better to use DFT methods to compare the relative energies

Q3. The MOs all look good – I wouldn’t have chosen that orientation to show them however (it’s a bit of a nit picking point but it would be better to see them at an angle to see some perspective). The reactivity is correctly described with reference to the HOMO. The IR stretches look fine and the effect of the pi-sigma* interaction is well analysed.

Q4. It seems that you stopped halfway through your answer at the end; perhaps this was due to time constraint, but otherwise make sure to check over what you have done before submission. R=Me is the correct choice here and your energy values are pretty good (especially the PM6 ones); for MM2 some values are a bit high, but it is more difficult to find the global minimum (as you will have seen in Q2). Some of your jmols don’t match the description – be careful to get the correct file name when putting in the code. Your calculations show (in terms of both energies and structures) that A=C and B=D when MOPAC calculations are performed – this is because when the carbonyl oxygen is close to the oxonium carbon, bonding interactions can be determined. In contrast in MM2 the bonds are fixed by the user at the beginning.

MP. The discussion of the energetics of the different isomers is good. This application of methods used in the earlier questions is what we hope to see in the more open ended questions. The NMR and IR data looks to be a reasonable match. It would be worth considering if the inaccuracies are due to conformational flexibility by seeing if there are any other low energy conformations which could contribute to the physical properties of the compounds. More deshielded nuclei would be expected to be further downfield (i.e. higher ppm); the reason that you’re other peaks appear to be more deshielded than the one at 52 is that they are all in aromatic systems. Since you calculated NMR spectra for both isomers it would have been nice to see if the calculation could be used to distinguish one from the other (given a spectrum of an unknown). This would involve comparison of the two sets of computational spectra against the experimental spectrum and seeing if one example gives a better fit. For this kind of error analysis it can be useful if it’s done graphically (bar charts are often used) – presentation of the data in tables is fine, but different approaches can be considered (perhaps by consulting reported computation NMR data).