| Polarization is the induction of a dipole in a molecule by an electric field. The interactions of a molecule with fields from neighbor molecules in condensed phase systems are essential in determining bonding and spectroscopy.;Noncovalent interactions should in principle be modeled with ab initio calculations. However, the use of such methods to follow dynamics remains impractical in systems which contain several hundreds of atoms. Pairwise additive potentials, which are fitted to get specific properties in neat liquids, fail in dissimilar envionments such as ligands in proteins and interfaces. The need for transferable potentials has fueled the development of more sophisticated polarizable models. In this thesis, we use classical mechanics with a proper treatment of polarization induction to model complex noncovalent effects.;The calculation of energetics and spectroscopic properties for even small molecules are non-trivial. Applying a novel electrostatic models to diatomic ligands (CO, O2, and NO) in heme proteins, and water, we have successfully predicted many experimental properties of interest. The spectrum of carbon monoxide (CO) liquid, ligand binding energies in heme proteins, and the dependence of ligand bond frequencies on external electric fields are reproduced quite accurately. A new polarizable potential for water, POLIR, yields water cluster properties such as frequency shifts and energetics in remarkable agreement with ab initio calculations. The structural and dynamical properties of liquid water and ice are in good agreement with experiments. The change in the H -- O -- H angle, and the frequency shifts of the bend, symmetric stretch and anti-symmetric normal modes, upon condensing and freezing are again in agreement with experiments. Finally, in support of recent experimental data, the combination bands in liquid water and ice are captured for the first time.;More generally, our results demonstrate that classical electrostatics with accurate treatment of the polarization effects can provide an alternative approach to quantum mechanics for a considerable simplification of some complex problems. The current approach has broad applications in the fields of drug discovery and protein folding, and protein-ligand and protein-protein interfaces where the electrostatics is of considerable significance. |
