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Title: Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition

Authors:
ORCiD logo [1];  [1];  [1]; ORCiD logo [2]; ORCiD logo [1]
  1. Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115, USA
  2. Department of Computational and Applied Mathematics, Rice University, Houston, Texas 77005, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1349362
Grant/Contract Number:
AC02-06CH11357
Resource Type:
Journal Article: Publisher's Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 146; Journal Issue: 9; Related Information: CHORUS Timestamp: 2018-02-15 01:34:59; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics
Country of Publication:
United States
Language:
English

Citation Formats

Molavi Tabrizi, Amirhossein, Goossens, Spencer, Mehdizadeh Rahimi, Ali, Knepley, Matthew, and Bardhan, Jaydeep P. Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition. United States: N. p., 2017. Web. doi:10.1063/1.4977037.
Molavi Tabrizi, Amirhossein, Goossens, Spencer, Mehdizadeh Rahimi, Ali, Knepley, Matthew, & Bardhan, Jaydeep P. Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition. United States. doi:10.1063/1.4977037.
Molavi Tabrizi, Amirhossein, Goossens, Spencer, Mehdizadeh Rahimi, Ali, Knepley, Matthew, and Bardhan, Jaydeep P. Tue . "Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition". United States. doi:10.1063/1.4977037.
@article{osti_1349362,
title = {Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition},
author = {Molavi Tabrizi, Amirhossein and Goossens, Spencer and Mehdizadeh Rahimi, Ali and Knepley, Matthew and Bardhan, Jaydeep P.},
abstractNote = {},
doi = {10.1063/1.4977037},
journal = {Journal of Chemical Physics},
number = 9,
volume = 146,
place = {United States},
year = {Tue Mar 07 00:00:00 EST 2017},
month = {Tue Mar 07 00:00:00 EST 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1063/1.4977037

Citation Metrics:
Cited by: 1work
Citation information provided by
Web of Science

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  • Theories of solvation free energies often involve electrostatic potentials at the position of a solute charge. Simulation calculations that apply cutoffs and periodic boundary conditions based on molecular centers result in center-dependent contributions to electrostatics energies due to a systematic sorting of charges in radial shells. This sorting of charges induces a surface-charge density at the cutoff sphere or simulation-box boundary that depends on the choice of molecular centers. We identify a simple solution that gives correct, center-independent results, namely the radial integration of charge densities. Our conclusions are illustrated for a Lennard-Jones solute in water. The present results canmore » affect the parametrization of force fields. 15 refs., 3 figs.« less
  • Steady-state and time-resolved emission measurements of the solvatochromic probe coumarin 153 are used to study solvation of a dipolar solute in nondipolar solvents such as benzene and 1,4-dioxane. Contrary to the predictions of dielectric continuum theories, the Stokes shifts (or nuclear reorganization energies) that accompany electronic excitation of this solute are substantial in such solvents (nearly 1000 cm{sup -1}). The magnitudes of the shifts observed in both nondipolar and dipolar solvents can be consistently understood in terms of the relative strength of the interactions between the permanent charge distributions of the solute and solvent molecules. (Information concerning these charge distributionsmore » is derived from extensive ab initio calculations on the solute and 31 common solvents). The dynamics of solvation in nondipolar solvents, as reflected in the time dependence of the Stokes shifts, is qualitatively like that observed in polar solvents. But, whereas the dynamics in polar solvents can be rather simply modeled using the solvents dielectric response as empirical input, no simple theories of this sort are currently capable of predicting the solvation dynamics in nondipolar solvents 52 refs., 14 figs., 4 tabs.« less
  • Accurate determination of absolute solvation free energy plays a critical role in numerous areas of biomolecular modeling and drug discovery. A quantitative representation of ligand and receptor desolvation, in particular, is an essential component of current docking and scoring methods. Furthermore, the partitioning of a drug between aqueous and nonpolar solvents is one of the important factors considered in pharmacokinetics. In this study, the absolute hydration free energy for a set of 239 neutral ligands spanning diverse chemical functional groups commonly found in drugs and drug-like candidates is calculated using the molecular dynamics free energy perturbation method (FEP/MD) with explicitmore » water molecules, and compared to experimental data as well as its counterparts obtained using implicit solvent models. The hydration free energies are calculated from explicit solvent simulations using a staged FEP procedure permitting a separation of the total free energy into polar and nonpolar contributions. The nonpolar component is further decomposed into attractive (dispersive) and repulsive (cavity) components using the Weeks-Chandler-Anderson (WCA) separation scheme. To increase the computational efficiency, all of the FEP/MD simulations are generated using a mixed explicit/implicit solvent scheme with a relatively small number of explicit TIP3P water molecules, in which the influence of the remaining bulk is incorporated via the spherical solvent boundary potential (SSBP). The performances of two fixed-charge force fields designed for small organic molecules, the General Amber force field (GAFF), and the all-atom CHARMm-MSI, are compared. Because of the crucial role of electrostatics in solvation free energy, the results from various commonly used charge generation models based on the semiempirical (AM1-BCC) and QM calculations [charge fitting using ChelpG and RESP] are compared. In addition, the solvation free energies of the test set are also calculated using Poisson-Boltzmann (PB) and Generalized Born model of solvation (GB), which are two widely used continuum electrostatic implicit solvent models. The protocol for running the absolute solvation free energy calculations used throughout is automated as much as possible, with minimum user intervention, so that it can be used in large-scale analysis and force field optimization.« less
  • Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for coarse grained models of electrolyte solution. Here, we provide rigorous definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation,more » comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to highly unphysical values for the solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation. We would like to thank Thomas Beck, Shawn Kathmann, Richard Remsing and John Weeks for helpful discussions. Computing resources were generously allocated by PNNL's Institutional Computing program. This research also used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. TTD, GKS, and CJM were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multi-program national laboratory operated by Battelle for the U.S. Department of Energy.« less
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