The Equivalent Potential Of Water Molecules For Electronic Structure Of Cysteine

The knowledge of electronic structure is essential in understanding a protein's properties and functions. 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. Because the first-principles, ab initio calculation of the electronic structure of protein is on its primary stage, there is no suitable equivalent potential of water molecules. 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. There are more than a hundred thousands of proteins, but all are made up of 20 amino acids. So for the electronic structure calculation of proteins, we only need to construct the equivalent potentials of 20 amino acids. As the first sample, we choose cysteine (Cys) which is relatively small. Cys has 14 atoms with a lateral chain of mercaptan.The first-principles, all-electron, ab initio calculations, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for cysteine (Cys). The process consists of three parts. First, the electronic structure of the cluster containing Cys 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 Cys with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of cysteine with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of cysteine with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the...