Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model

Mehdizadeh Rahimi, Ali; Molavi Tabrizi, Amirhossein; Goossens, Spencer; Knepley, Matthew G.; Bardhan, Jaydeep P.

doi:10.1002/qua.25771

Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model

Journal Article · Fri Oct 12 00:00:00 EDT 2018 · International Journal of Quantum Chemistry

DOI:https://doi.org/10.1002/qua.25771· OSTI ID:1479564

Mehdizadeh Rahimi, Ali ^[1]; Molavi Tabrizi, Amirhossein ^[2]; Goossens, Spencer ^[1]; Knepley, Matthew G. ^[3]; ^[4]

Department of Mechanical Engineering Northeastern University Boston Massachusetts
Department of Physics Northeastern University Boston Massachusetts
Department of Computer Science SUNY Buffalo Buffalo New York
GlaxoSmithKline Collegeville Pennsylvania

Abstract

We demonstrate that the solvation‐layer interface condition (SLIC) continuum dielectric model for molecular electrostatics, combined with a simple solvent‐accessible‐surface‐area (SASA)‐proportional model for nonpolar solvent effects, accurately predicts solvation entropies of neutral and charged small molecules. The SLIC/SASA model has only seven fitting parameters in total and achieves this accuracy using a training set with only 20 compounds. Despite this simplicity, solvation free energies and entropies are nearly as accurate as those predicted by the more sophisticated Langevin dipoles solvation model. Surprisingly, the model automatically reproduces the negligible contribution of electrostatics to the solvation of hydrophobic compounds. Opportunities for improvement include nonpolar solvation, anion solvation entropies, and heat capacities. More molecular realism may be needed for these quantities. To enable a future, explicit‐solvent‐based assessment of the SLIC/SASA implicit‐solvent model, we predict solvation entropies for the Mobley test set, which are available as Supporting Information.

View Accepted Manuscript (Publisher)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1479564

Journal Information:: International Journal of Quantum Chemistry, Journal Name: International Journal of Quantum Chemistry Journal Issue: 1 Vol. 119; ISSN 0020-7608

Publisher:: Wiley Blackwell (John Wiley & Sons)Copyright Statement

Country of Publication:: United States

Language:: English

References (69)

Application of the thin-shell formulation to the numerical modeling of Stern layer in biomolecular electrostatics Manzin, Alessandra; Bottauscio, Oriano; Ansalone, Domenico Patrizio Journal of Computational Chemistry, Vol. 32, Issue 14 https://doi.org/10.1002/jcc.21896	journal	August 2011
Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models Cumberworth, Alexander; Bui, Jennifer M.; Gsponer, Jörg Journal of Computational Chemistry, Vol. 37, Issue 7 https://doi.org/10.1002/jcc.24235	journal	November 2015
Contribution of Hydration to Protein Folding Thermodynamics Makhatadze, George I.; Privalov, Peter L. Journal of Molecular Biology, Vol. 232, Issue 2 https://doi.org/10.1006/jmbi.1993.1416	journal	July 1993
Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution Cabani, Sergio; Gianni, Paolo; Mollica, Vincenzo Journal of Solution Chemistry, Vol. 10, Issue 8 https://doi.org/10.1007/BF00646936	journal	August 1981
Designing electrostatic interactions in biological systems via charge optimization or combinatorial approaches: insights and challenges with a continuum electrostatic framework Radhakrishnan, Mala L. Theoretical Chemistry Accounts, Vol. 131, Issue 8 https://doi.org/10.1007/s00214-012-1252-5	journal	July 2012
FreeSolv: a database of experimental and calculated hydration free energies, with input files Mobley, David L.; Guthrie, J. Peter Journal of Computer-Aided Molecular Design, Vol. 28, Issue 7 https://doi.org/10.1007/s10822-014-9747-x	journal	June 2014
On the calculation of electrostatic interactions in proteins Gilson, Michael K.; Rashin, Alexander; Fine, Richard Journal of Molecular Biology, Vol. 184, Issue 3 https://doi.org/10.1016/0022-2836(85)90297-9	journal	August 1985
Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects Miertuš, S.; Scrocco, E.; Tomasi, J. Chemical Physics, Vol. 55, Issue 1 https://doi.org/10.1016/0301-0104(81)85090-2	journal	February 1981
A view of thermodynamics of hydration emerging from continuum studies Rashin, Alexander A.; Bukatin, Michael A. Biophysical Chemistry, Vol. 51, Issue 2-3 https://doi.org/10.1016/0301-4622(94)00060-3	journal	August 1994
The statistical-thermodynamic basis for computation of binding affinities: a critical review Gilson, M. K.; Given, J. A.; Bush, B. L. Biophysical Journal, Vol. 72, Issue 3 https://doi.org/10.1016/S0006-3495(97)78756-3	journal	March 1997
Implicit solvent models Roux, Benoı̂t; Simonson, Thomas Biophysical Chemistry, Vol. 78, Issue 1-2 https://doi.org/10.1016/S0301-4622(98)00226-9	journal	April 1999
Optimized atomic radii for protein continuum electrostatics solvation forces Nina, Mafalda; Im, Wonpil; Roux, Benoı̂t Biophysical Chemistry, Vol. 78, Issue 1-2 https://doi.org/10.1016/S0301-4622(98)00236-1	journal	April 1999
Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations Anandakrishnan, Ramu; Drozdetski, Aleksander; Walker, Ross C. Biophysical Journal, Vol. 108, Issue 5 https://doi.org/10.1016/j.bpj.2014.12.047	journal	March 2015
Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali Journal of Chemical Theory and Computation, Vol. 13, Issue 6 https://doi.org/10.1021/acs.jctc.6b00832	journal	May 2017
Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity–Basity Scale Revisited Reif, Maria M.; Hünenberger, Philippe H. The Journal of Physical Chemistry B, Vol. 120, Issue 33 https://doi.org/10.1021/acs.jpcb.6b02156	journal	May 2016
Free energy calculations: Applications to chemical and biochemical phenomena Kollman, Peter. Chemical Reviews, Vol. 93, Issue 7 https://doi.org/10.1021/cr00023a004	journal	November 1993
Electrostatics in biomolecular structure and dynamics Davis, Malcolm E.; McCammon, J. Andrew Chemical Reviews, Vol. 90, Issue 3 https://doi.org/10.1021/cr00101a005	journal	May 1990
Field-Extremum Model for Short-Range Contributions to Hydration Free Energy Pomogaeva, Anna; Chipman, Daniel M. Journal of Chemical Theory and Computation, Vol. 7, Issue 12 https://doi.org/10.1021/ct200575c	journal	October 2011
Hydration Energy from a Composite Method for Implicit Representation of Solvent Pomogaeva, Anna; Chipman, Daniel M. Journal of Chemical Theory and Computation, Vol. 10, Issue 1 https://doi.org/10.1021/ct400894j	journal	November 2013
Introducing Charge Hydration Asymmetry into the Generalized Born Model Mukhopadhyay, Abhishek; Aguilar, Boris H.; Tolokh, Igor S. Journal of Chemical Theory and Computation, Vol. 10, Issue 4 https://doi.org/10.1021/ct4010917	journal	March 2014
Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations Mobley, David L.; Bayly, Christopher I.; Cooper, Matthew D. Journal of Chemical Theory and Computation, Vol. 5, Issue 2 https://doi.org/10.1021/ct800409d	journal	January 2009
The AGBNP2 Implicit Solvation Model Gallicchio, Emilio; Paris, Kristina; Levy, Ronald M. Journal of Chemical Theory and Computation, Vol. 5, Issue 9 https://doi.org/10.1021/ct900234u	journal	July 2009
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models Sitkoff, Doree; Sharp, Kim A.; Honig, Barry The Journal of Physical Chemistry, Vol. 98, Issue 7 https://doi.org/10.1021/j100058a043	journal	February 1994
Macroscopic models of aqueous solutions: biological and chemical applications Honig, Barry; Sharp, Kim; Yang, An Suei The Journal of Physical Chemistry, Vol. 97, Issue 6 https://doi.org/10.1021/j100108a002	journal	February 1993
Continuum based calculations of hydration entropies and the hydrophobic effect Rashin, Alexander A.; Bukatin, Michael A. The Journal of Physical Chemistry, Vol. 95, Issue 8 https://doi.org/10.1021/j100161a002	journal	April 1991
Reevaluation of the Born model of ion hydration Rashin, Alexander A.; Honig, Barry The Journal of Physical Chemistry, Vol. 89, Issue 26 https://doi.org/10.1021/j100272a006	journal	December 1985
A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes Rashin, Alexander A.; Namboodiri, Krishnan. The Journal of Physical Chemistry, Vol. 91, Issue 23 https://doi.org/10.1021/j100307a038	journal	November 1987
Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations Jean-Charles, Arald; Nicholls, Anthony; Sharp, Kim Journal of the American Chemical Society, Vol. 113, Issue 4 https://doi.org/10.1021/ja00004a079	journal	February 1991
Thermodynamics of Ion Hydration as a Measure of Effective Dielectric Properties of Water Noyes, Richard M. Journal of the American Chemical Society, Vol. 84, Issue 4 https://doi.org/10.1021/ja00863a002	journal	February 1962
Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P. Journal of the American Chemical Society, Vol. 135, Issue 45 https://doi.org/10.1021/ja406995j	journal	October 2013
Convergence of Molecular and Macroscopic Continuum Descriptions of Ion Hydration Ashbaugh, Henry S. The Journal of Physical Chemistry B, Vol. 104, Issue 31 https://doi.org/10.1021/jp0015067	journal	August 2000
Predicting Aqueous Free Energies of Solvation as Functions of Temperature Chamberlin, Adam C.; Cramer, Christopher J.; Truhlar, Donald G. The Journal of Physical Chemistry B, Vol. 110, Issue 11 https://doi.org/10.1021/jp057264y	journal	March 2006
Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models Hess, Berk; van der Vegt, Nico F. A. The Journal of Physical Chemistry B, Vol. 110, Issue 35 https://doi.org/10.1021/jp0641029	journal	September 2006
Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules Mobley, David L.; Dill, Ken A.; Chodera, John D. The Journal of Physical Chemistry B, Vol. 112, Issue 3 https://doi.org/10.1021/jp0764384	journal	January 2008
Extension of a Temperature-Dependent Aqueous Solvation Model to Compounds Containing Nitrogen, Fluorine, Chlorine, Bromine, and Sulfur Chamberlin, Adam C.; Cramer, Christopher J.; Truhlar, Donald G. The Journal of Physical Chemistry B, Vol. 112, Issue 10 https://doi.org/10.1021/jp076682v	journal	March 2008
Understanding the Surface Potential of Water Kathmann, Shawn M.; Kuo, I-Feng William; Mundy, Christopher J. The Journal of Physical Chemistry B, Vol. 115, Issue 15 https://doi.org/10.1021/jp1116036	journal	April 2011
Composite Method for Implicit Representation of Solvent in Dimethyl Sulfoxide and Acetonitrile Pomogaeva, Anna; Chipman, Daniel M. The Journal of Physical Chemistry A, Vol. 119, Issue 21 https://doi.org/10.1021/jp5098519	journal	December 2014
Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations ^† Mobley, David L.; Bayly, Christopher I.; Cooper, Matthew D. The Journal of Physical Chemistry B, Vol. 113, Issue 14 https://doi.org/10.1021/jp806838b	journal	April 2009
Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies Purisima, Enrico O.; Sulea, Traian The Journal of Physical Chemistry B, Vol. 113, Issue 24 https://doi.org/10.1021/jp9020799	journal	June 2009
New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects Marten, Bryan; Kim, Kyungsun; Cortis, Christian The Journal of Physical Chemistry, Vol. 100, Issue 28 https://doi.org/10.1021/jp953087x	journal	January 1996
On the Validity of Electrostatic Linear Response in Polar Solvents Åqvist, Johan; Hansson, Tomas The Journal of Physical Chemistry, Vol. 100, Issue 22 https://doi.org/10.1021/jp953640a	journal	January 1996
Evaluation of Solvent Effects in Isotropic and Anisotropic Dielectrics and in Ionic Solutions with a Unified Integral Equation Method: Theoretical Bases, Computational Implementation, and Numerical Applications Mennucci, B.; Cancès, E.; Tomasi, J. The Journal of Physical Chemistry B, Vol. 101, Issue 49 https://doi.org/10.1021/jp971959k	journal	December 1997
Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model Florián, Jan; Warshel, Arieh The Journal of Physical Chemistry B, Vol. 103, Issue 46 https://doi.org/10.1021/jp992041r	journal	November 1999
Continuum Solvation Models: What Else Can We Learn from Them? Mennucci, Benedetta The Journal of Physical Chemistry Letters, Vol. 1, Issue 10 https://doi.org/10.1021/jz100506s	journal	April 2010
High-Throughput Prediction of the Hydration Free Energies of Small Molecules from a Classical Density Functional Theory Liu, Yu; Fu, Jia; Wu, Jianzhong The Journal of Physical Chemistry Letters, Vol. 4, Issue 21 https://doi.org/10.1021/jz401787p	journal	October 2013
New applications of integral equations methods for solvation continuum models: ionic solutions and liquid crystals Cancès, Eric; Mennucci, Benedetta Journal of Mathematical Chemistry, Vol. 23, Issue 3/4, p. 309-326 https://doi.org/10.1023/A:1019133611148	journal	January 1998
Free Volume and Entropy in Condensed Systems III. Entropy in Binary Liquid Mixtures; Partial Molal Entropy in Dilute Solutions; Structure and Thermodynamics in Aqueous Electrolytes Frank, Henry S.; Evans, Marjorie W. The Journal of Chemical Physics, Vol. 13, Issue 11 https://doi.org/10.1063/1.1723985	journal	November 1945
The Free Energy of Hydration of Gaseous Ions, and the Absolute Potential of the Normal Calomel Electrode Latimer, Wendell M.; Pitzer, Kenneth S.; Slansky, Cyril M. The Journal of Chemical Physics, Vol. 7, Issue 2 https://doi.org/10.1063/1.1750387	journal	February 1939
Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models? Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew The Journal of Chemical Physics, Vol. 127, Issue 15 https://doi.org/10.1063/1.2771171	journal	October 2007
Continuous surface charge polarizable continuum models of solvation. I. General formalism Scalmani, Giovanni; Frisch, Michael J. The Journal of Chemical Physics, Vol. 132, Issue 11 https://doi.org/10.1063/1.3359469	journal	March 2010
Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation Zhou, Huan‐Xiang The Journal of Chemical Physics, Vol. 100, Issue 4 https://doi.org/10.1063/1.466406	journal	February 1994
Charge penetration in dielectric models of solvation Chipman, Daniel M. The Journal of Chemical Physics, Vol. 106, Issue 24 https://doi.org/10.1063/1.474048	journal	June 1997
A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics Cancès, E.; Mennucci, B.; Tomasi, J. The Journal of Chemical Physics, Vol. 107, Issue 8 https://doi.org/10.1063/1.474659	journal	August 1997
A stringent test of the cavity concept in continuum dielectrics Papazyan, Arno; Warshel, Arieh The Journal of Chemical Physics, Vol. 107, Issue 19 https://doi.org/10.1063/1.475059	journal	November 1997
Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee The Journal of Chemical Physics, Vol. 137, Issue 12 https://doi.org/10.1063/1.4752735	journal	September 2012
Modeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticle Delgado, Alain; Corni, Stefano; Goldoni, Guido The Journal of Chemical Physics, Vol. 139, Issue 2 https://doi.org/10.1063/1.4812680	journal	July 2013
Domain decomposition for implicit solvation models Cancès, Eric; Maday, Yvon; Stamm, Benjamin The Journal of Chemical Physics, Vol. 139, Issue 5 https://doi.org/10.1063/1.4816767	journal	August 2013
Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions Bardhan, Jaydeep P.; Knepley, Matthew G. The Journal of Chemical Physics, Vol. 141, Issue 13 https://doi.org/10.1063/1.4897324	journal	October 2014
Communication: Accurate hydration free energies at a wide range of temperatures from 3D-RISM Misin, Maksim; Fedorov, Maxim V.; Palmer, David S. The Journal of Chemical Physics, Vol. 142, Issue 9 https://doi.org/10.1063/1.4914315	journal	March 2015
The role of Stern layer in the interplay of dielectric saturation and ion steric effects for the capacitance of graphene in aqueous electrolytes Daniels, Lindsey; Scott, Matthew; Mišković, Z. L. The Journal of Chemical Physics, Vol. 146, Issue 9 https://doi.org/10.1063/1.4976991	journal	March 2017
Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration Hofer, Thomas S.; Hünenberger, Philippe H. The Journal of Chemical Physics, Vol. 148, Issue 22 https://doi.org/10.1063/1.5000799	journal	June 2018
Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms Wagoner, J. A.; Baker, N. A. Proceedings of the National Academy of Sciences, Vol. 103, Issue 22 https://doi.org/10.1073/pnas.0600118103	journal	May 2006
Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface Tabrizi, Amirhossein Molavi; Knepley, Matthew G.; Bardhan, Jaydeep P. Molecular Physics, Vol. 114, Issue 16-17 https://doi.org/10.1080/00268976.2016.1198503	journal	March 2016
Derivative-free optimization for parameter estimation in computational nuclear physics Wild, Stefan M.; Sarich, Jason; Schunck, Nicolas Journal of Physics G: Nuclear and Particle Physics, Vol. 42, Issue 3 https://doi.org/10.1088/0954-3899/42/3/034031	journal	February 2015
Biomolecular electrostatics—I want your solvation (model) Bardhan, Jaydeep P. Computational Science & Discovery, Vol. 5, Issue 1 https://doi.org/10.1088/1749-4699/5/1/013001	journal	January 2012
Dielectric response of the water hydration layer around spherical solutes Schaaf, Christian; Gekle, Stephan Physical Review E, Vol. 92, Issue 3 https://doi.org/10.1103/PhysRevE.92.032718	journal	September 2015
Analytical molecular surface calculation Connolly, M. L. Journal of Applied Crystallography, Vol. 16, Issue 5 https://doi.org/10.1107/S0021889883010985	journal	October 1983
The Many Roles of Computation in Drug Discovery Jorgensen, W. L. Science, Vol. 303, Issue 5665 https://doi.org/10.1126/science.1096361	journal	March 2004
Using simulation to study solvation in water Lynden-Bell, R. M.; Rasaiah, J. C.; Noworyta, J. P. Pure and Applied Chemistry, Vol. 73, Issue 11 https://doi.org/10.1351/pac200173111721	journal	January 2001

Similar Records

Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model

Journal Article · Tue Aug 23 20:00:00 EDT 2022 · Journal of Chemical Theory and Computation · OSTI ID:1968997

Graphical Gaussian Process Regression Model for Aqueous Solvation Free Energy Prediction of Organic Molecules in Redox Flow Battery

Journal Article · Mon Jun 14 20:00:00 EDT 2021 · Physical Chemistry Chemical Physics. PCCP · OSTI ID:1817885

Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model

Citation Formats

References (69)

Similar Records

Related Subjects