Biophysical J 567A-567A (January 2007)



A Model for Polarizable and Ionizable Water

Judith Herzfeld, Michael Blank, Stacy Z. Dai

Dept. of Chemistry MS #015
Brandeis University, Waltham MA 02454-9110



Abstract

Water is often a functionally important part of the active sites of proteins. In order to understand how it can play more than a structural role, it is necessary to take its polarizability and its ionizability into account. Of course, this is best done by quantum mechanics. However, most systems of interest are sufficiently large that it would be useful to have models that are less computer intensive. Here we present such a model. Whereas conventional water models use a fixed array of partial charges to mimic the electrostatic moments of a water molecule, ionizability requires protons with full charges and both ionizability and polarizability require that the submolecular particles be mobile. Our model includes, in addition to protons with charge +1, also oxygen cores (nucleus plus the 1s electron pair) with charge +6, and valence electron pairs with charge -2. The pseudo potentials devised for the interactions between these particles are super-coulombic for electron-electron interactions, reflecting Pauli exclusion, and sub-coulombic for nucleus-electron interactions, reflecting the diffuse distributions of the electrons. Parameters have been found for these pseudopotentials that produce stable water monomers, water dimers, hydroxide ions and hydronium ions, all with bond angles and bond lengths in close agreement with experiment. In addition, the potentials generalize to give stable structures of ammonia, ammonium ion and methane that are in similar agreement with experiment. Thus the positions of the energy minima have been fit very well by our pseudopotentials. Although no attempt has been made to fit the depths and breadths of the energy minima, the energies for water dissociation, proton transfer and hydrogen bonding agree reasonably well with experiment, as do the force constants for water stretching and bending vibrations. (Supported by a grant from the NIBIB.)