The Equivalent Potential Of Water Molecules For The Electronic Structures Of Lysine And Histidine

Proteomics is a new important field in life science. It will promote greatly our understanding of life activities, and give us valuable clue in the research of diagnosis and treatment, as well as in the development of new medicines. Currently, there are mainly experimental studies in the proteomics. According to quantum mechanics, however, the knowledge of electronic structure is essential for understanding the properties and functions of material or molecule. The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort greatly, while the calculation precision is kept. This makes the the first-principles, all-electron, ab initio calculation of the electronic structure of protein a reality. Up to day, the electronic structures of three proteins have been obtained. However, the former calculations did not include solvent influence due to limited computational conditions and the following reasons: water molecules are usually quivering, turning and fungible at high speed in action with protein. There is no fixed chemical bonding between water molecules and protein in solution. The effect of water molecules on protein is a kind of average force, which mainly influences the three-dimensional structure of protein.In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct an equivalent potential of water molecules for protein's electronic structure calculation. The equivalent potential must be simple, easy-use, effective and with little additional computational effort. Because it is impossible to add a large amount of water molecules to the calculation. The first-principles, all-electron, ab initio calculations, based on the density functional theory, have been performed to construct such equivalent potentials of water molecules for lysine (Lys.~+) and histidine (His). The process consists of three parts. First, the electronic structure of the cluster containing amino acid and water molecules is calculated. By adjusting the positions of water molecules, the geometric structure of the cluster having minimum total energy is determined. Then, based on the structure, the electronic structure of amino acid with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of amino acid with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of amino acid with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of an amino acid is obtained. The major effect of water molecules on the electronic structures of lysine (Lys.~+) and histidine (His) is raising the occupied eigenvalues and broadening energy gaps. The effect of water molecules on the...