Talk:Cbl08:module 1
Q1. All of your calculated energies are good. The discussion of kinetic control in the dimerisation reaction is good and the illustration nicely shows the orbital interaction. The contributors to strain in the different molecules are correctly identified. The bending strain specifically relates to deviation from ideal bond angles so the difference is that the angles in the bicyclic ring deviate from 120 degrees to a greater extent. You should be careful when comparing energies obtained with molecular mechanics: strictly speaking you can only compare isomers because for different molecules the energy scale is not the same.
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Q2. Your structures are good and your endeavour to try different modelling methods is shrewd in this case since there are limitations in the basic molecular mechanics methods that effect accuracy. It is also good that you have discussed your efforts for finding the lowest energy conformation; you might have more luck finding different conformations if you change more than one atom to generate different starting points: Just moving the carbonyl oxygen leaves the rest of the molecule in its original conformation so the easiest path to a conformational minimum is just to spring back to how it was before being moved. The carbonyl group can’t “chelate” to magnesium because chelation involves binding by more than one atom of a ligand: it is better described as coordinating or ligating oxygen. Note that these compounds do not contain pyridine rings, but positively-charged pyridinium rings (this is why the reagent is so electrophilic).
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Q3. Your energy values are close but the “down” isomer (compound 10) is in fact the more stable conformation. The approach is very good – finding the different 6-ring conformations to find overall the global minimum. Also, the analysis of the structural differences between the atropisomers is well addressed. It is not possible to compare MM2 calculated energies of the alkane and alkene because these are not isomeric compounds – using DFT you could do this.
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Q4. This question was very well answered – the MOs look good, although you should have reported the energy you found for the molecule. As well the values for the IR stretch are correct and your explanations for both the nucleophilicity of the syn-alkene and the C-Cl bond strength are right.
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MP. The mini project fits the requirements well (diastereomers with rigid structures). I’m not sure how you decided which atoms correspond to which. Was the 13C NMR spectrum fully assigned in the publication? It seems as though a better comparison would be to order them by increasing size in both cases if they are not already assigned. Remember that the numerical labelling given to each atom by chemdraw/gaussian has no real meaning and is totally random; it certainly won’t match any existing numbering system for natural products or other compounds that are well studied. You didn’t mention how these compounds were distinguished experimentally; since they were obtained by crystallisation I would imagine X-ray diffraction analysis was used to give conclusive assignment. Alternatively it could be worked out by NMR because Ha and Hb are close in space in the “endo” isomer but not the “exo” isomer: this will give rise to different coupling constants based on the dihedral angles but also the through-space relationship can be analysed by a technique called nuclear Overhauser effect spectroscopy (NOESY).