Thermodynamic and Transport Properties of Alkanes (C_nH_2n+2; n = 5-8)

In the present work, we have utilized "alchemical" approaches to study the thermodynamic properties of four alkane molecules: pentane, hexane, heptane, and octane in water. We have used thermodynamic integration (TI) and free energy perturbation (FEP) based methods: TI, TI-cubic, Bennett acceptance ration (BAR), and Multistate Bennett acceptance ratio (MBAR)to estimate the solvation free energy of alkane molecules in water at 300 K for 21 distinct coupling parameter values (λ). For each alkane molecule, the estimated values of solvation free energy using the different methods are in close agreement, which ensures the reliability of our study. Convergence of the calculation has also been examined through time series plots in both forward and reverse directions. Our study shows that the solvation free energy increases with increasing size of the alkane molecules, which is also supported by estimation of solvent accessible surface area (SASA). The self diffusion coefficients of both solutes and solvent molecules; and shear viscosity of the systems have been estimated at 293 and 300 K temperatures. The self diffusion coefficient of the alkane molecules decreases with increase in size and shear viscosity increases with chain length as expected. The estimated values of diffusion and shear viscosity are in close agreement with the previously reported values.