Eur. Phys. J. B 52, 255-263 (2006)
https://doi.org/10.1140/epjb/e2006-00284-8

The equivalent potential of water molecules for electronic structure of cysteine

Pohl Institute of Solid State Physics, Tongji University, Shanghai, 200092, P.R. China

Corresponding author: ^a xmwang1981@163.com

Received: 14 April 2006
Published online: 11 July 2006

Abstract

In order to get more reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. The first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of Cys. The process consists of three steps. First, the electronic structure of the cluster containing Cys and water molecules is calculated. Then, based on the structure, the electronic structure of Cys with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Cys with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Cys with the potential of dipoles is close to that of water molecules. The calculations show that the major effect of water molecules on Cys' electronic structure is lowering the occupied electronic states by about 0.032 Ry, and broadening energy gap by 16%. The effect of water molecules on the electronic structure of Cys can be simulated by dipoles potential.