Thermodynamic and transport properties of amoxicillin

We have carried out MD simulations of amoxicillin, a drug molecule used as antibacterial agent, in water and ethanol to study thermodynamic properties like solvation free energy and transport phenomena like diffusion, viscosity. The free energy of solvation of amoxicillin in water and ethanol have been estimated at 310 K using thermodynamic integration (TI) and free energy perturbation (FEP) based methods. It has been obtained that the free energy of solvation of amoxicillin in water is higher by ≈ 105 kJ/mol in TIP3P model than in ethanol. We have also reported the solvent accessible surface area (SASA) of solute as well as the hydrogen bonds between solute and solvent for different solvents. The analysis of SASA and hydrogen bond provides more insight on effect of solvent environment in solvation process of amoxicillin. We have also estimated the diffusion coefficient and our results show that diffusion coefficients of amoxicillin depends on solvent environment, as expected, and it is higher in water than that of ethanol. Also, applying the idea of system size dependence of diffusion coefficient, the viscosity coefficient of water and solution of amoxicillin in water have also been estimated. Furthermore, the effects of temperature on diffusion has been studied. The estimated values of self-diffusion coefficients of water are in good agreement with previously reported experimental data within ≈13.5%.