Talk:Mod:mtr09mod1

Overall, I like you way of presenting the data, especially the Jmols, which prevents cluttered tables and give the data some clarity.

Correct energies, correct analysis of endo-exo-thermodynamics-kinetics.
Correct analysis of torsion energy.
You used product 3 and 4, but list product C and D in the table.
Very detailed analysis of the energy components of 3 and 4. But a bit more on the selectivity of the reaction itself would be great.

You've shown some understanding about the difference between MM2 and MMFF94, which isn't always appreciated by undergraduates.
"For Molecule 9, this antiperiplanar relation is lost, and replaced by a highly unfavourable synperiplanar arrangement. The unfavourable nature of these interactions causes Molecule 9 to undergo isomerisation to form Molecule 10" Why is the antiperiplanar arrangement is better than the synperiplanar? You'll need to explain this, perhaps with a diagram.
"very large rings effectively have allyic alkene bonds" should be "very large rings effectively have allylic alkene bonds"?
"The value of total energy is lower for the hydrogenated product than for the its alkene precursor", should be "higher". The correct analysis when comparing 10 and hydrogenated-10 should yield bend and 1,4 WDW energies as the main contributor.
You must balance your equation when comparing the energies of different system!

The reason that the MOs aren't strictly symmetrical is because the optimisation went wrong and slightly remove the symmetry. Re-optimisation via a different method helps!
"the electrophillic chlorocarbene species" should be "the electrophillic dichlorocarbene species"
You didn't specify whether you saw the interaction described by Rzepa in your MOs calculation. You also need to be more explicit in explaining the different in reactivity between the two double bond. What is controlling the reactivity with electrophiles? And how the listed factors influence that.
"Upon optimisation, it was noted that the saturated ring became slightly more bent". It actually went into staggered conformation, which is preferred for alkanes.
Dspace link could be more obvious rather than being reference. No penalty here, but it would certainly help the marking process.
You completely ignored the bond lengths while analysing bond strength.
Your frequencies for 13 are off. Did you optimise the structure using DFT prior to frequencies calculation? Still the argument was correct.

"The disparity between methods is evident for larger systems, such as the ones we are currently analysing". Actually the real reason why MM2 is completely inadequate here is because it can't deal with either the oxonium (non-classical cation) and the interaction between that and the lone pair rbitals on OAc.
Correct choice of Me group, but you didn't discuss why we can't go with just OH.
Your MM2 Jmols are fine, but your numbering is different from that in the question (A and A'). Since the oxonium ring has a very different shape from cyclohexane, axial and equatorial don't have any meaning anymore.
PM6 Jmols: A is wrong (the CH2OMe is now swinged in to stabilise the oxonium while OAc is pointing away), B' is most certainly wrong as all these groups get lumped up, this is where the software fails and you have to be the brain.
Well spotted A = C, B = D. Your calculation is probably correct, but the much easier one is K = exp(-dG/RT). The conclusion is still the same! Remember the difference for C/C' and D/D' calculated by MM2? It's very very different from the PM6 results.

Your question isn't well defined. You elaborated later on, but maybe a short summary at the beginning would help. It's a lot of work you've done and readers may find it difficult to follow.
Minimisation using just AM1 might be a problem, as NMR calculations are highly sensitive to conformational changes.
I think you're trying to handle too much data at once, which somewhat affect the effectiveness of the analysis and data presentation.
Correct focus on the relevant carbons.
15N NMR: what are the literature values? Quite hard to find, actually. SO we can't check if the prediction is good! If you forget the 4-membered ring, the one N is next to a carbonyl and a C-O2C, the other is next to a carbonyl and a C-CO2 (very much like in proteins, for which 15H NMR data is plentiful).
IR spectra is very tricky in this case, as predictions aren't accurate enough, and the region in question normally has other peaks in them.