Calculations of accurate energies in proteins with QM/MM methods

Abstract: Accurate calculation of energies for protein reactions is a hard problem. There are many reasons for wanting to calculate these energies, e.g. ligand design and the study of enzyme reactions. There are two major problem involved in these kinds of calculations. First, the large number of local minima in proteins introduces uncertainties when studying single structures. Second, the size of proteins prohibits the use of accurate quantum mechanical (QM) methods. This forces us to either to study small QM models of the active site or to turn to combined QM and molecular mechanics (QM/MM) methods that incorporate the whole protein. This thesis deals with these two problems. In particular, the effect of active-site size is studied, as well as the importance of sampling. The first problem is studied by looking at the effect of varying the size of the QM region in both QM-only and QM/MM calculations. The effect of the surroundings is also tested. The second problem is addressed by studying methods to perform free-energy perturbation calculations at the QM/MM level. Approximate methods to obtain QM/MM free-energies are also developed and tested.