View source for Talk:Mod:EllynIII


Cope: Short and to the point introduction, explaining what we’re about to do. Careful though - the Cope rearrangement isn’t a cycloaddition, so we can’t lump it together with the Diels Alder.

Table & Figure legends - good. Also Jmol & log files of all the conformers you found - again good. Perhaps some comparisons of geometry between HF/DFT methods? There are differences: the ordering of the lowest energy conformers change when reoptimised with the DFT method. You give a plausible explanation of why the anti conformers should be lower in energy, but maybe a couple of MO pictures/diagrams would help here too? The gauche 3 conformer is still low energy compared to the other gauche conformations - any ideas why this might be? Again, MOs might help!

IR & thermochemistry data all present & correct.

Transition state calculations clearly described & results look good. Appropriate references too. For the QST2 “The atom numbers were defined so that a bond was formed between atom 1 and 6 and a bond broken between 3 and 4 in the product” - a picture here of the orientation & labelling of the molecules in the QST2 setup would help us see what you mean.

‘Negative’ (actually imaginary) frequency means transition state, but why? (Essentially, a result of the foce constant / 2nd derivative of the potential energy surface along the reaction coordinate being -ve. A -ve 2nd derivative = a maximum on the curve, = a TS)

Good description of IRC and the results all look good. Activation energies also look correct, but energies in Hartree only really need to be quoted to 5/6 d.p.

Diels Alder: Again, good clear introduction, & explanation of symmetry. Perhaps use ‘diene’ & ‘dienophile’ if you want to be generic and not keep saying ‘butadiene/ethene’?

MOs and transition states all look fine, and clear to see how they relate to symmetry/MOs of reactants. IRC is also very good.

Comparison of methods (AM1/DFT) is very good, though differences between MOs might be easier to see if all molecules had the same orientation (I know this is difficult to achieve, but it’d help).

“The extra stabilisation arises from the interaction of the carbonyl π* orbitals and the п-orbital of the developing double bond.” - Presuming you’re referring to ‘secondary orbital overlap’ here. Good description of why it may/may not be responsible for regioselectivity, but again, a schematic diagram might help us visualise what you mean better.

Van der Waals radius + interaction?

Activation energies again look good. IRC also nice to see - the animations of the full reaction path are impressive.

Overall: A clearly laid out report, with a nice logical progression of ideas and flow to the work. Results all look correct, with some nice additions (e.g. IRCs showing the full reaction path) that also show you’ve understood the concepts and the reasons why we take the steps we do. As small areas to improve, a couple more literature references (particularly during introductions/background) and some schematic diagrams when you reference particular conformations, atoms or orbitals would be good.