Simulation of water potential for the electronic structure of serine

First-principles, all-electron, ab initio calculations have been performed to construct an equivalent water potential for the electronic structure of serine （Ser） in solution. The calculation is composed of three steps. The first step is to search for the configuration of the Ser _ nH2O system with a minimum energy. The second step is to calculate the electronic structure of Ser with the water molecule potential via the self-consistent cluster-embedding method （SCCE）, based on the result obtained in the first step. The last step is to calculate the electronic structure of Set with the dipole potential after replacing the water molecules with dipoles. The results show that the occupied states of Ser are raised by about 0.017 Ry on average due to the effect of water. The water effect can be successfully simulated by using the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method.

The equivalent potential of water molecules for electronic structure of lysine

In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct a potential of water molecules for protein’s electronic structure calculation. The lysine is a hydrophilic amino acid. It is positively charged (Lys+) in neutral water solution. The first-principles, all-electron, ab initio calcula-tions, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for lysine (Lys+). The process consists of three parts. First, the electronic structure of the cluster containing Lys+ 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 Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of Lys+ with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained. The major effect of water molecules on lysine’s electronic structure is raising the occupied eigenvalues about 0.5032 eV, and broadening energy gap 89%. The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.