Molecular Dynamics Study of Transport Properties of Cysteine in Water

Abstract: Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five different temperatures (288 K, 293 K, 303 K, 313 K, 323 K) under the pressure of 1 bar is studied using GROMACS. OPLS AA force field parameters are used throughout the simulation. The system under study consists of 3 cysteine molecules (mole fraction 0.003) as solute and 1039 water molecules (mole fraction 0.997) as solvent. The radial distribution functions (RDFs) for five different combinations of atoms of solvent-solvent and solute solvent molecules are studied for structural analysis. At least two or more distinct peaks are observed in RDFs plots implying that there are interactions between atoms of solvent solvent and solute solvent at least up to two co ordination shells. The self diffusion coefficients of solute and solvent are determined exploiting mean square displacement (MSD) in Einsteins equation. The self diffusion coefficients are used to calculate the binary diffusion coefficients by means of Darkens relation. The calculated values of self diffusion and binary diffusion coefficients are compared with available experimental values and they agreed within 12 percent. The temperature dependency of diffusions are demonstrated via Arrhenius plots and with the help of these plots activation energies for diffusions are calculated which agreed with experimental results within 13 percent.