Date of Award

Summer 8-15-2013

Author's School

Graduate School of Arts and Sciences

Author's Department

Biology & Biomedical Sciences (Computational & Systems Biology)

Degree Name

Doctor of Philosophy (PhD)

Degree Type



This dissertation focuses on the development of polarizable molecular mechanics (MM) force field models for the third-row transition metal (TM) ions. These TM ions perform important structural and chemical functions in a wide range of organic and biological environments because of the unique properties of the 3d orbitals. Being able study these systems in silico can provide a tremendous amount of information that is difficult to obtain through experiments. However, the standard treatment of ions in traditional MM models has shown to be insufficient for describing the d-shell electronic effects. In this work, empirical models for TM electronic effects are derived from the valence bond (VB) theory and the angular overlap model (AOM). The TM potential functions are incorporated into the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) MM force field. A consistent polarizable electrostatics model is applied between metal and ligand sites at all interaction distance, enabling the study of ligand association / dissociation and other dynamic events. Specifically, theories are presented in the context of Ni(II), Cu(II) and Zn(II) ions. Parameters are obtained by fitting the TM models to gas-phase ab initio computations. Finally, results from molecular dynamics simulations of aqueous ions and select type 1 copper proteins (plastocyanin and azurin) are analyzed. Evidence from this study suggests that explicit description of d-shell electronic effect can significantly improve the performance of MM models. This allows one to perform more reliable investigations on complex TM systems than can be achieved with traditional MM methods but without the computational expense of ab initio calculations.


English (en)

Chair and Committee

Garland Marshall

Committee Members

Anders Carlsson, Cynthia Lo, Liviu Mirica, Jay Ponder, Scott Wildman