Talk:Mod:jlm2012

Q1

It would be much easier for marker if you follow the numbering in the question: 1, 2, 3 and 4.

Your MM2 energies for 1 and 2 are correct. Here you mentioned you tried to compare the dihedral angles, but did not show the data. It is the norm in scientific writing to present the data before your analysis so the reader can form their own conclusions, which hopefully are the same as yours.

· Correct analysis on the dimerisation being kinetic controlled, but we expect you to state the obvious that Diels-Alder reactions are often kinetic controlled (unless at high temp.) and provide an explanation for the endo-selectivity.

"The hydrogenation can take place on the six member ring or on the five member ring". To me, both double bonds are in five-memberred rings. You also should have stated that now we only study the hydrogenation of 2.

Again, you have the correct MM2 energies for 3 and 4. "The product 3 is thermodynamically less stable than the product 4", by how much?

"simple bond" should be "single bond". "This is because the angles between the double bond and the simple bonds in the molecule 3 are really smaller than the optimal value (107° instead of 122°)", what are the corresponding values in 4?

The largest difference between 3 and 4, as I look at your table, is the bend energy. In any case, all these arise from the fact that in 3 the double bond is part of the highly strained bicyclic structure. A list of bond angles and their deviation from optimal values would have quickly identified the part of the molecule responsible for the higher energy of 3 compared to 4.

Overall, you have the correct results, but the presentation of data, analysis and understanding of the results are slightly underpar.

Q2

Again, using the numbering system in the question would help here.

Your energies for 9 and 10 are wrong. I had a look at your optimised structures and they are local minima rather than global minima.
Your understanding of the 'hyperstable' alkene concept is rather shaky. This is a phenomenon often associated with bridged medium rings which contain significant steric strain. This strain could be partially relieved by double bonds, particularly at bridgehead positions. Your idea of comparing the energy of 9/10 and their hydrogenated product is sound, but you'll need to take into account the energy of H₂ to balance the equation.

"in a kinetic sens" should be "in a kinetic sense"

MMFF94 calculation, the last part of this question, is missing.

Q3

"Chloro-methanonaphtalene" should be "Dichloromethanonaphthalene".

"The first raw shows the orbitals calculated by the laptop and the second raw the orbitals calculated by the computer in the library." Surely you mean "row", not "raw".

They look similar to me, just inverted phase. Good job spotting in any case.

The all important answer to the question after HOMO calculation: which double bond is more reactive to electrophilic carbene? is unanswered.

Correct vibrational frequencies for the two double bonds in 12. Again, exo-endo terminology isn't just wrong, it makes me having to second guessing what you mean. IR pictures look dubious.

You completely missed the interaction between C-Cl bond and the anti double bond, which shows in HOMO. This interaction is also responsible for the extra stability (higher vibrational frequency) of this double bond. All these can also be corroborated by examining the bond lengths of the double bonds and the C-Cl bond in the diene 12 and the two possible hydrogenated products.

Overall, again you did the job but did not provide the adequate analysis of the results.

Q4

R = Me is the better choice here. OH groups tend to form H-bonds, which can unnecessarily complicate the calculations.

Your A' and B' optimised structures are wrong, hence their energies.

Your A and B structures from PM6 look fine, but you did not appreciate the key difference between MM2 and PM6: PM6 is a quantum calculation while MM2 isn't. Consequently, PM6 try to form a bond between the acetyl and the carbocation when it can, but MM2 will not because it was told there is no bond there. Another effect is that with PM6, optimised structure of A/B is the same as C/D.

No neighbouring-group stablisation energy was calculated.

Rationalisation of stereospecificity: you need to appreciate the two possible mechanistic pathways in each case, and differentiate between their energies (intermediate) B vs B', D vs D', to determine the stereochemical outcomes of the reactions.

Mini project

Extra 5% is given for choosing your own problem. I like the idea of using modelling to predict/match stereochemical outcomes, which is what we do frequently in reality. But as with every other problem you've done, you would have greatly benefited if you've come in and have a chat with either Matt (PhD demonstrator) or myself.

The relative stereochemical outcome of the reaction is actually only determined by the last step from 4 to 5, which is actually under thermodynamic control. By going over every previous intermediates, you multiplied the workload unnecessarily.

Interesting outcomes with MM2 and PM6 with the final diastereoisomers. After looking at your optimised structure using MM2, I get a whooping 12.5 kcal/mol in favour of the trans product.

Total mark: 42/100

Part of the reason for the not-so-great informal mark, I think, is that you're an Erasmus student and are not under real pressure to perform here. You also did not come to the computational lab and discuss the problems/project with us.

I think the benefits of the lab to experimentalists, whom I myself am one, are great and it would be a shame if we leave you with a poor experience. I would suggest you to contact Patricia Hunt about actually attending the lab sessions for Module 2 and 3. You don't need to come to them all, but talking to us once or twice would certainly be very beneficial. Regarding Module 1, we'll have another run from 14/11 and if you wish to come and discuss the points in this work, you're most welcomed to do so. You can also contact me directly via email and I'll try to arrange some time for the discussion.