The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators.
The development and parameterization of a solvent potential of mean force designed to reproduce the hydration thermodynamics of small molecules and macromolecules aimed toward applications in conformation prediction and ligand binding free energy prediction is presented. The model, named SGB/NP, is based on a parameterization of the Surface Generalized Born continuum dielectric electrostatic model using explicit solvent free energy perturbation calculations and a newly developed nonpolar hydration free energy estimator motivated by the results of explicit solvent simulations of the thermodynamics of hydration of hydrocarbons. The nonpolar model contains, in addition to the more commonly used solvent accessible surface area term, a component corresponding to the attractive solute-solvent interactions. This term is found to be important to improve the accuracy of the model, particularly for cyclic and hydrogen bonding compounds. The model is parameterized against the experimental hydration free energies of a set of small organic molecules. The model reproduces the experimental hydration free energies of small organic molecules with an accuracy comparable or superior to similar models employing more computationally demanding estimators and/or a more extensive set of parameters.
Gallicchio
Emilio
E
Department of Chemistry and Chemical Biology, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, New Jersey 08854-8087, USA. emilio@hpcp.rutgers.edu
Zhang
Linda Yu
LY
Levy
Ronald M
RM
D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D006838:Hydrocarbons / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D006838:Hydrocarbons; D012997:Solvents; D014867:Water