Talk:Mod:rom3112
1.1 Good energies and results. Might just slightly expand the section discussing kinetic v s thermodynamic control.
1.2 Your energies for molecule 5 are very much higher than we expect. I suspect you have not defined your pyridinium nitrogen as having a positive charge! It makes all the difference. The O-CH2 region has several conformation, and you may have to hunt for the lowest! The model could be improved by directly involving the Grignard, although MM2 does not have parameters! Any of the MO-based methods could handle this however via a transition state calculation (see module 3). Molecule 7 again has high energies (again, lack of N+ ?). You might speculate on whether Mg is attracted to a carbonyl and whether (from the appropriate angle of approach) an amine is repelled. The lowest energy of 7 appears to be that with the carbonyl below the plane of the ring.
1.3 Your energy for 11 is absolutely spot on! But that for 10 is way too high! Looking at your geometry (which we can do via the Jmol model you have kindly provided), it appears as if the geometry at the carbonyl is very odd! Angles of < 90? It must be some sort of artificial minimum allowed by MM2 by nevertheless physically unrealistic. At least you have noticed that its the bend that is up the spout!
1.4 You got three of the four energies exactly the same as my model answers (which do not prove they are the best of course). The only one where we differ is the equatorial trans decalin, which comes out lower than the axial. In your discussion you allude to, but do not mention the role of entropy in accelerating an intramolecular vs intermolecular reaction. You also mention that substituents are "closer". You should indicate the distances in order to make this quantitative.
1.5. You do well by by noting the distortions visible in the optimised geometry of the diene (one points up, the other does not)! But in your analysis of the alkene, you record the C-H stretches, whereas of course the interaction is with the C=C bond, and you should therefore record the C=C stretches. You claim the alkene has no C=C stretches? That is certainly not true, although they are predicted at 1761 and 1741. You mention the HOMO-1 is stabilised, again you could quote its energy to show how much by.
2. You conclude that molecule A corresponds to the data from the literature. But there is no statistical analysis to illustrate this. For example, what is the mean deviation between theory and expt for both A and B? If you read the two citations we give you, you have examples of how to perform this analysis. You should get < 2 ppm for a good fit, and > 2 ppm for a less good fit, with perhaps larger outliers. You let yourself down a bit here by the relatively minimal discussion in this section. The five references you cite are not in the accepted format, and indeed it is not possible to check them, since you quote only the titles and no journals or page numbers!
You have presented your project well; it looks nice! A little more discussion and it would have been very good.--Rzepa 17:20, 3 November 2008 (UTC)
