Dr. François Dehez
Equipe de dynamique des assemblages membranaires, Unité mixte de recherché
Nancy Université
Cedex, France

Monday, November 24, 2008
3:00 pm (CT)
3269 Beckman Institute

Abstract

Standard force fields used to study biomolecular systems only provide an implicit representation of the mean intermolecular polarization. This approximation has proven to be reasonable, but remains inaccurate in several instances. The explicit introduction of polarization effects in molecular simulations is mandatory to describe with an appropriate precision the properties of biomolecular systems along a trajectory. A variety of methods have been proposed to obtain polarizable models for biomolecules with a common objective: the balance between accuracy and tractability. One possible strategy relies on the use of atomic polarizabilities derived from the induction energy mapped around the molecule. In the framework of optimally partitioned electric properties (OPEP) [1], implicitly interacting models consisting of distributed charge-flow and isotropic dipole polarizabilities are shown to describe correctly the anisotropic pattern of the overall molecular polarizability. However necessary, ensuring the reproduction of the properties of the isolated molecule is not sufficient to guarantee a proper description of the intermolecular polarization. The classical interaction model, appropriate for large intermolecular distances, does account for short-range electronic exchange on the induction energy. It is shown that the latter contribution could be essentially recovered through an ad hoc damping of the classical expression of the polarization potential. Performance of the models are further probed in the challenging test cases of cation-π binding and the association of a divalent calcium ion with water, formalde-hyde and formate ion, where induction effects are notoriously large [2,3]. The resulting individual electrostatic and induction contributions to the binding energies agree reasonably well with the corresponding terms of a symmetry-adapted perturbation theory (SAPT) expansion.