Chemistry 8003: Computational Chemistry

Midterm

1. Listed below are a number of different theoretical models. This problem consists of a series of properties you would like to calculate for various molecular systems. For each property, explain what level or levels of theory might be most useful. If there is more than one possibility for a useful level, describe which, if any, you think would be best and explain your answer. If there are any levels that would clearly not be applicable for calculation of the property (perhaps because they are physically incapable of its calculation), list them and explain why. Finally, it is conceivable you might use multiple methods, and you are free to describe that, together with your rationale, as well. Be concise but detailed in your explanations.

Possible models: Molecular mechanics with MM3 force field.

Molecular mechanics with OPLS force field.

Semiempirical ZINDO method.

Semiempirical AM1 method.

Semiempirical PM3 method.

a) Lowest energy structure for cyclodecane (25 points).

b) UV spectrum (i.e., energies to reach excited electronic states) of iron-oxo porphyrin (25 points).

c) Calculation of the gas-phase activation energy for the atmospherically important reaction HO* + HOO* -> H2O + O2 (25 points).

d) "Flexibility" of chymotrypsin in aqueous solution (a typical way to measure this is to examine the mean-square-displacement of the [[alpha]]-carbons in the peptide backbone from their average positions during the course of a dynamics simulation) (25 points).

e) Gas-phase dipole moment for the lowest energy structure of the sugar D-lyxose (25 points).

f) Pictures of the [[pi]] orbitals for pyridine (25 points).

2. Implicit in the above problem was that none of the properties being calculated was available experimentally. Given that, explain how you might assess the quality of the answers you get from your calculations in different instances. You don't have to do this on a molecule by molecule basis! Rather, I am looking for some general discussion of how you decide on the trustworthiness of your results. A good answer will provide some hypothetical situations for discussion (e.g., I could do x and compare to y and if situation z were to be true I would draw conclusion w, etc.) and/or include specific examples which may or may not be derived from the above problems (50 points).