Simulation of water potential for the electronic structure of serine

Abstract

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 Ser 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.