Talk:Ss2310:Module 3

Introduction short introduction - could be more developed.

Cope rearrangement Some conformers optimised - not all of them. Good discussion about their relative energy. But what do you mean by “the experimentally calculated values”? Values are either measured experimentally or calculated theoretically. Note that, experimentally, we cannot measure an absolute energy but only an energy difference. The values in the Appendix are calculated values! Your frequency calculation was successful but how did you check (using the frequency results) that the optimised structure is a minimum? TS optimisations were successful but how did you check they are TS? Your IRC calculation was successful but what did you learn from it? You should conclude a preferred mechanism from your results.

Diels Alder “In order to visualise the MOs a frequency calculation was carried out” The frequency calculation is used to determine the type of stationary point you have located, orbitals are computed during the optimization. A minimum energy structure should have only real (positive) frequencies, you show excerpt from an output giving one imaginary frequency indicating a TS. This is in the section under cis- butadiene optimization but it is labelled Diels-Alder, so is it in the wrong place? The link to your AM1 cis-butadiene molecule shows a B3LYP/3-21G [4 + 2] TS optimization. You say the TS HOMO is asymmetric but the orbital you show is symmetric wrt the Cs plane. “As bonds are being formed and broken at the same time, this mechanism is symmetric and synchronous.” A stationary point structure does not confirm this (although the presence of equal distance forming bonds is an indication). To prove it you would have to look at the imaginary mode and run an IRC to connect these two points on the potential energy surface. “However, the results of -605.61036757 and -605.60359123 hartree for the Endo and Exo respectively do not agree with the theory that the Endo will experience a lower energy.” But the figure quoted for the endo is lower in energy (by 4.25 Kcal/mol). “This may be due to an error in how the calculation was run in Gaussian, due to positioning of the original molecule.” You did do the calculations correctly and the results are fine. You show a diagram with the geometry of the exo state, it would be good to add the endo measurements as well for discussion. The geometry of the TS is important for kinetically favoured reactions, the steric hindrance of the exo product is therefore of no consequence. Why don’t you try and point out some evidence from ab initio calculations of effects you illustrate in the diagrams, e.g. secondary orbital overlap.

Overall Try to elaborate on how ab initio calculation agree or disagree with empirical thoeretical concepts such as FMO theory or the Woodward-Hoffmann rules. It is good to see some correlation diagrams, but relate these to the calculations.