Talk:Mod:SAMROWE001

Q1

• Correct calculation for the dimers, but we're looking for some analysis as well. Where do you think the difference in energy come from? Which part of the molecules is responsible for it? The two hydrogens you mentioned is part of it, but there's more. You'll need to go back to the meaning of each component of the overall energy.
• Again, which part of the monohydrogenated compounds is responsible for the difference in bend energy?

Q2

• I appreciate that you discussed the twisted-boat conformers and explained how you arrived at the final optimised structures.

A bit more analysis on the MMFF94 data and components would be great here. Does it give the same structure as MM2?

• I think you 'get' the concept of hyperstable alkenes, but will need to explain it more clearly. Why didn't you show more calculation results of the hydrogenated compound? Can you compare that with the alkene (BIG CLUE: balance the equation!).

Q3

• Your picture size is good, but from this point of view I can't see the other half of the molecule. This is important when looking at MOs, so please adjust the pictures.
• A bit more elaboration on the σ*-π interaction (specifying each orbitals are involved and the consequences which you will observe later with your vibrational frequencies calculation) would be great.

Q4

• Which complex interactions are we talking about? and why can't MM2 handle them?
• From the energies for intermediate C/C' and D/D' can you calculate their equilibrium constants and predict the diastereoselectivity of the reactions?
• Your MM2 structures (which I can't find) aren't the lowest in energy, although your PM6 energies are close (not quite yet). However, it's the analysis and explanation that matter here.
• It would be very important to have a figure showing which structures are A/A' B/B' C/C' and D/D'. I already think you're using a different system from the one in the question.
• " it is able to detect that ring B' shows many unfavourable orbital interactions and therefore distorts the entire geometry to produce a structure which is very similar to that of ring B. " I don't think there is unfavourable interaction here. B is just so more stable. Did you start off with structure B from MM2? Again, since I'm not seeing the jmol, it's all guess work.
• The whole purpose of this question is to let students find out the origin of the diastereoselectivity observed for this kind of reaction. From the energies for intermediate C/C' and D/D' can you calculate their equilibrium constants and predict the diastereoselectivity of the reactions?

Overall

I think you made a good start, but the analysis side is still lacking for really good mark. Nevertheless, I hope the feeback help and would welcome any further discussion.

After Marking:

Q1: Your energy values are all correct and the analysis of the contributions to strain is broadly correct. For compounds 3 and 4 the main difference is in the alkene bond angles rather than the bond angles specifically within the bridged bicyclic part. What you say about kinetic and thermodynamic control is correct – you can’t really say much more about the hydrogenation than you have without more information about the reaction conditions and knowledge of the transition state energies (which would require DFT methods).

Q2. Your energy values and the structures of your global minima are correct. Although you have the right answer it would have been good to see how you got there – e.g. showing some higher energy conformations you found along the way. For example, although 6-rings often adopt chair conformations this is not always the most stable form (sometimes twist-boat or boat can be formed). Bending strain specifically refers to deviation from ideal bond angles so there will be some angles in isomer 9 that deviate more than in isomer 10. The definition of hyperstable alkenes is good and the qualitative analysis of strain in the hydrogenated form is a nice extra – it is not really possible to compare energy values using MM methods because these are not isomeric species (also you need to include the energy of hydrogen to get a balanced equation).

Q3. This question was well answered - the MOs and stretches are correct and both the regioselectivity and the pi-sigma* interaction are fully explained. The only thing to mention is that it is worth inlcuding the energy values you get for all calculations as these are sometimes used to evaluate the calculations.

Q4. R=Me is the correct choice and the energy values you have using PM6 are pretty good; Some of the MM2 results are a bit off (there should still be a significant difference between A/B and A’/B’ (>10kcal/mol) ; without the structures it is hard to see why your energies are different – there is quite a degree of flexibility even in this relatively small system. As you have found, when using MOPAC methods A=C etc. You’re explanation for this is correct – MOPAC can determine bonding interactions if the appropriate atoms are close, whereas MM cannot. NB: The Burgi-Dunitz angle is 107.

MP. Your calculated spectral data all seems to give a good match to the reported values – the main thing you can take away from this is that the geometry minimisation has accurately give the main conformation of the various structures. Displaying the results in tables is fine, but for this kind of analysis a graphical representation can be beneficial (usually a bar chart) in the relevant literature. Since you calculated data for two different isomers it would have been interesting to see if you could differentiate them using these results – i.e. could you tell which unknown isomer you have given the NMR spectrum. The main reason for calculating the 13C NMR spectrum rather than the 1H NMR spectrum is that prediction of the 1H spectrum is more difficult. The last part of the MP was interesting because it is somewhat similar to the typical activities of computational chemists looking at reaction mechanisms: As in this paper, it is often important to consider different conformations of reactants to work out reaction mechanisms – although ultimately the key energy is probably that of the transition state because a higher energy conformation may be more reactive (consider elimination of HBr from bromocyclohexane – this can only occur if Br is axial). Overall, you have amassed an impressive amount of results but it may have been better to focus more on data analysis than acquisition. What you have definitely shown is that this set of compounds can be very accurately modelled.