Molecular dynamic study and the effect of solvent dielectric constant on structure of heme-containing protein Cytochrome c in different media

The solvent dielectric constant is considered an important factor in determining the properties of the heme-containing protein cytochrome c in solution. Therefore, we investigate solvents effects on the relative energies, dipole moment values, and structural properties of water, methanol, and ethanol surrounding heme c (HEC), by using molecular dynamics simulation. In this study, we substitute the Iron atom of HEC with other metal atoms such as Cobalt, Nickel, Copper and Zinc and polar solvent effect has been performed using Onsager model. Calculations were carried out with the GAUSSIAN 98 program based on density functional theory (DFT) at B3LYP/6-31G* level. We have compared gas phase and solvent calculations