Talk:Mod:Loftus
Q1. Your energy values are all correct. The reason the endo product is formed is a kinetic effect, more specifically, it is a secondary orbital effect: in the endo TS orbitals not involved in bond formation are capable of interacting with and stabilising the TS as a whole. Bending strain is indeed the major difference between the monohydrogenated compounds, this type of strain is defined as strain caused by deviation from ideal bond angle; you can probably see from your model structures that the bond angles in the bicyclic double bond are further from the expected 120 degrees for sp2 carbon.
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Q2. The structures look good (although you have drawn the enantiomer of the first pyridinium – since this has the same physical properties it isn’t that big a problem) and you have correctly explained the stereochemistry. In terms of minimisation of energy it is not simply a matter of minimising a number of times, but also using different starting points for the calculations to explore the full conformational landscape. You are right to say that the available molecular mechanics force fields cannot account for magnesium – this is because magnesium is not a recognised atom-type (its parameters are unknown to the program). It is possible to modify the parameters so that you can include previously unavailable atom-types. A nitpicking point: stereochemistry is spelt with an e (i.e. not steriochemistry)!
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Q3. The energy values are good and assignment of the lowest energy conformation is correct. The Jmols you have given for molecules i and j are in fact both one of the pyridinium intermediates and not the molecules described! You have correctly defined hyperstable alkenes but it is not possible to compare the energies of the alkanes and alkenes using MM2 because they are now different molecules not isomers; the origin of the unusually high strain in the alkane is likely due to torsional/steric clashes. You could calculate energies using DFT and get energy values to compare.
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Q4. You calculated the energy of the molecule using a number of different methods but then only gave the energy value for the MM2 calculation – make sure you state the key numbers you obtain. The MO diagrams look good as you say the location of the HOMO on the syn alkene shows that this is the most nucleophilic. The alkene reactivities relate in a sense to the pi orbital strength whereas the whole double bond contains a sigma bond as well – so the overall bond strength may be different compared to the reactivity (your IR results suggest that the syn double bond is stronger overall). Values from correlation tables are not really “literature values” in any case; you can just say that a result is as expected for a C-Cl bond or you could find a specific example (maybe structurally similar or better still the actual experimental data for the molecule) and compare its IR stretch.
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MP. This is a very good project. The choice of reaction was good as the product is structurally rigid and not excessively big. Probably the most flexible part of the molecule is the methoxy, methyl side chain and as you observed this was the part giving the greatest error. Maybe there are a few conformations available to this group that contribute in different amounts to the overall energy and physical properties. The analysis of error in the NMR calculation was conducted very well, this comparison of two sets of calculated data to the lit data is, I think, the most scientific way to judge whether you can distinguish between them. It is also what you would do if you weren’t sure about the structure of something you made but you had NMR data to analyse and compare to. The mechanistic discussion is good, it is a proposal that you could analyse further DFT by calculating the two transition state energies using DFT.