Talk:Mod:yudanchenmod3

Introduction

Absent.

Cope rearrangement

Few conformers successfully optimised - not all of them. Good discussion about their relative energy. “All vibrational frequencies are real and positive, indicating the molecule is fully optimised.” Be careful: very small force and displacement are required for your geometry to be optimised. All real frequencies means that your optimised geometry is a minimum on the potential energy surface. On the other hand, one imaginary frequency means that your optimised structure is a transition state on the potential energy surface. You should check it when optimising stationary points. It is a good idea to optimise the last points of your IRC calculations but what did you conclude from these minimisations? Which conformers do the TS structures connect? According to your results, what is the activation energy for each mechanism? What is the preferred mechanism? Are the computed values in agreement with the experimental ones?

Diels-Alder cycloaddition

How do the forming distances compare to 2x C vdW distance which indicates the limit at which the two electron clouds start interacting? The fact it is shorter than this but longer than the C­C equilibrium distance shows the structure is between reactant and product, i.e. a TS. The lowest real frequency is symmetry breaking, suggesting that this motion is uphill in energy (and would not occur). Which fragment orbitals combine to form the product HOMO/LUMO, what are the symmetry rules for these combinations? Which conformer is the most stable in the maleic anhydride + cyclohexadiene calculation? What are the differences in the structures and why might one be more stable than the other. Is there any support from your computations to illustrate some of these effects? Extra discussion on this: <http://pubs.acs.org/doi/abs/10.1021/ar0000152>

Conclusion

Too many extracts from the output file. Choose only the relevant parts. There's very little discussion to demonstrate your understanding, or to answer the questions set in the exercise.