Component Of Solvation Free Energy Research Articles

Efficient Computation of the Electrostatic Component of Solvation Free Energy via a Two-Point Padé Approximation.

We develop an efficient method to compute the electrostatic component of the solvation free energy via the two-point Padé approximation. The Padé approximant uses four parameters to describe the electrostatic free energy change of the solvation process, which could be readily determined from four thermodynamic properties obtained in two simulations, namely, the first- and second-order free energy gradients of any two states. Therefore, instead of sampling at multiple intermediate states, only two states, e.g., electrostatically fully solvated and desolvated, are needed to determine the Padé approximant and compute the corresponding free energy contribution. Applications to several model systems, including both neutral and charged species, show that the method can accurately produce electrostatic solvation free energy. The method would be very useful to save computational cost in applications in which accurate but expensive energy functions like quantum mechanics are used.

Determination of cubic equation of state parameters for pure fluids from first principle solvation calculations

AbstractA new method for estimation of parameters in cubic equations of state from ab initio solvation calculations is presented. In this method, the temperature‐dependent interaction parameter a(T) is determined from the attractive component of solvation free energy, whereas the volume parameter b is assumed to be that of solvation cavity. This method requires only element‐specific parameters, i.e., atomic radius and dispersion coefficient, and nine universal parameters for electrostatic and hydrogen‐bonding interactions. The equations of state (EOS) parameters so determined allow the description of the complete fluid phase diagram, including the critical point. We have examined this method using the Peng–Robinson EOS for 392 compounds and achieved an accuracy of 43% in vapor pressure, 17% in liquid density, 5.4% in critical temperature, 11% in critical pressure, and 4% in critical volume. This method is, in principle, applicable to any chemical species and is especially useful for those whose experimental data are not available. © 2008 American Institute of Chemical Engineers AIChE J, 2008

A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes

Reliable computer simulations of complex biological environments such as integral membrane proteins with explicit water and lipid molecules remain a challenging task. We propose a modification of the standard generalized Born theory of homogeneous solvent for modeling the heterogeneous dielectric environments such as lipid/water interfaces. Our model allows the representation of biological membranes in the form of multiple layered dielectric regions with dielectric constants that are different from the solute cavity. The proposed new formalism is shown to predict the electrostatic component of solvation free energy with a relative error of 0.17% compared to exact finite-difference solutions of the Poisson equation for a transmembrane helix test system. Molecular dynamics simulations of melittin and bacteriorhodopsin are carried out and performed over 10 ns and 7 ns of simulation time, respectively. The center of melittin along the membrane normal in these stable simulations is in excellent agreement with the relevant experimental data. Simulations of bacteriorhodopsin started from the experimental structure remained stable and in close agreement with experiment. We also examined the free energy profiles of water and amino acid side chain analogs upon membrane insertion. The results with our implicit membrane model agree well with the experimental transfer free energy data from cyclohexane to water as well as explicit solvent simulations of water and selected side chain analogs.