Performance of molecular dynamics simulation for predicting of solvation free energy of neutral solutes in methanol

Citations Over Time

Abstract

Abstract In this study, molecular dynamics simulation was applied for calculating solvation free energy of 16 solute molecules in methanol solvent. The thermodynamic integration method was used because it was possible to calculate the difference in free energy in any thermodynamic path. After comparing results for solvation free energy in different force fields, COMPASS force field was selected since it had the lowest error compared to experimental result. Group-based summation method was used to compute electrostatic and van der Waals forces at 298.15 K and 1 atm. The results of solvation free energy were obtained from molecular dynamics simulation and were compared to the results from Solvation Model Density (SMD) and Universal Continuum Solvation Model (denoted as SM8), which were obtained from other research works. Average square-root-error for molecular dynamics simulation, SMD and SM8 models were 0.096091, 0.595798, and 0.70649. Furthermore, the coefficient of determination ( R 2 ) for molecular dynamics simulation was 0.9618, which shows higher accuracy of MD simulation for calculating solvation free energy comparing to two other models.

Related Papers

• → Nonpolar Solvation Free Energies of Protein−Ligand Complexes(2010)37 cited
• → Solvation free energy arithmetic for small organic molecules(2023)2 cited
• → A Solvation/Desolvation Indicator Based on van der Waals Interactions between Solvents and Porphyrins(2018)9 cited
• → Comparative Study of Implicit and Explicit Solvation Models for Probing Tryptophan Side Chain Packing in Proteins(2012)4 cited
• → Contribution of Solvation Energy in Protein‐Peptide Recognition Systems(2001)3 cited