Development of polarizable force fields for proteins

University of Minnesota Ph.D. dissertation. December 2008. Major: Chemistry. Advisors: Prof. Jiali Gao and Prof. Donald G. Truhlar.1 computer file (PDF); xiii, 238 pages.This work describes the development of the polarizable force field for proteins based on classical mechanics, electronic structure theory and the combined quantum mechanical molecular mechanical method. In the first model, the classical force field is augmented with the explicit polarization energy term yielding a polarizable intermolecular potential function (PIPF). The polarizable atom sites in the system respond to the electric field by generating induced dipole moment at each site. The PIPF potential is optimized for amides and alkanes which are building blocks of proteins. The molecular dynamics simulations using the PIPF potential yield comparable or better energetics and geometries of the model compounds. In order to speed up the convergence of the induced dipole moments in the PIPF potential when all intramolecular interactions are included, we proposed a coupled polarization matrix inversion and iteration method (CPII). We were able to achieve convergence within 15 iterations for all the systems under consideration in which the iterative method shows divergence or oscillation. The second model, called the explicit polarization model (X-Pol), accounts for the polarization and charge transfer effects by treating all the fragments of the system using electronic structure theory. A variational version of the X-Pol potential is derived which facilitates the calculation of analytical gradient of energy needed for molecular dynamics simulations. Furthermore, the X-Pol potential is augmented with the buffer zone by calculating the two-electron Coulomb integrals between adjacent fragments in protein. The introduction of buffer zone in the X-Pol potential improves the convergence and the transferability of semiempirical parameters in the X-Pol potential. The molecular dynamics simulation of a solvated bovine pancreatic trypsine inhibitor reveals significant polarization and charge transfer effects in the protein