Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

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

Abstract

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.

Authors:
 [1];  [2];  [1];  [3]; ORCiD logo [4]
+ Show Author Affiliations
  1. Department of Mechanical Engineering Northeastern University Boston Massachusetts
  2. Department of Physics Northeastern University Boston Massachusetts
  3. Department of Computer Science SUNY Buffalo Buffalo New York
  4. GlaxoSmithKline Collegeville Pennsylvania
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1479564
Resource Type:
Publisher's Accepted Manuscript
Journal Name:
International Journal of Quantum Chemistry
Additional Journal Information:
Journal Name: International Journal of Quantum Chemistry Journal Volume: 119 Journal Issue: 1; Journal ID: ISSN 0020-7608
Publisher:
Wiley Blackwell (John Wiley & Sons)
Country of Publication:
United States
Language:
English

Citation Formats

Mehdizadeh Rahimi, Ali, Molavi Tabrizi, Amirhossein, Goossens, Spencer, Knepley, Matthew G., and Bardhan, Jaydeep P. Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model. United States: N. p., 2018. Web. doi:10.1002/qua.25771.
Copy to clipboard
Mehdizadeh Rahimi, Ali, Molavi Tabrizi, Amirhossein, Goossens, Spencer, Knepley, Matthew G., & Bardhan, Jaydeep P. Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model. United States. https://doi.org/10.1002/qua.25771
Copy to clipboard
Mehdizadeh Rahimi, Ali, Molavi Tabrizi, Amirhossein, Goossens, Spencer, Knepley, Matthew G., and Bardhan, Jaydeep P. Fri . "Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model". United States. https://doi.org/10.1002/qua.25771.
Copy to clipboard
@article{osti_1479564,
title = {Solvation thermodynamics of neutral and charged solutes using the solvation‐layer interface condition continuum dielectric model},
author = {Mehdizadeh Rahimi, Ali and Molavi Tabrizi, Amirhossein and Goossens, Spencer and Knepley, Matthew G. and Bardhan, Jaydeep P.},
abstractNote = {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.},
doi = {10.1002/qua.25771},
journal = {International Journal of Quantum Chemistry},
number = 1,
volume = 119,
place = {United States},
year = {Fri Oct 12 00:00:00 EDT 2018},
month = {Fri Oct 12 00:00:00 EDT 2018}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Accepted Manuscript (Publisher)
Publisher's Version of Record
https://doi.org/10.1002/qua.25771
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Using simulation to study solvation in water
journal, January 2001

  • Lynden-Bell, R. M.; Rasaiah, J. C.; Noworyta, J. P.
  • Pure and Applied Chemistry, Vol. 73, Issue 11
  • DOI: 10.1351/pac200173111721

Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules
journal, January 2008

  • Mobley, David L.; Dill, Ken A.; Chodera, John D.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 3
  • DOI: 10.1021/jp0764384

Optimized atomic radii for protein continuum electrostatics solvation forces
journal, April 1999

Generalising the mean spherical approximation as a multiscale, nonlinear boundary condition at the solute–solvent interface
journal, March 2016

  • Tabrizi, Amirhossein Molavi; Knepley, Matthew G.; Bardhan, Jaydeep P.
  • Molecular Physics, Vol. 114, Issue 16-17
  • DOI: 10.1080/00268976.2016.1198503

Application of the thin-shell formulation to the numerical modeling of Stern layer in biomolecular electrostatics
journal, August 2011

  • Manzin, Alessandra; Bottauscio, Oriano; Ansalone, Domenico Patrizio
  • Journal of Computational Chemistry, Vol. 32, Issue 14
  • DOI: 10.1002/jcc.21896

Understanding the Surface Potential of Water
journal, April 2011

  • Kathmann, Shawn M.; Kuo, I-Feng William; Mundy, Christopher J.
  • The Journal of Physical Chemistry B, Vol. 115, Issue 15
  • DOI: 10.1021/jp1116036

A simple method for the calculation of hydration enthalpies of polar molecules with arbitrary shapes
journal, November 1987

  • Rashin, Alexander A.; Namboodiri, Krishnan.
  • The Journal of Physical Chemistry, Vol. 91, Issue 23
  • DOI: 10.1021/j100307a038

The Free Energy of Hydration of Gaseous Ions, and the Absolute Potential of the Normal Calomel Electrode
journal, February 1939

  • Latimer, Wendell M.; Pitzer, Kenneth S.; Slansky, Cyril M.
  • The Journal of Chemical Physics, Vol. 7, Issue 2
  • DOI: 10.1063/1.1750387

Electrostatics in biomolecular structure and dynamics
journal, May 1990

  • Davis, Malcolm E.; McCammon, J. Andrew
  • Chemical Reviews, Vol. 90, Issue 3
  • DOI: 10.1021/cr00101a005

New applications of integral equations methods for solvation continuum models: ionic solutions and liquid crystals
journal, January 1998

  • Cancès, Eric; Mennucci, Benedetta
  • Journal of Mathematical Chemistry, Vol. 23, Issue 3/4, p. 309-326
  • DOI: 10.1023/A:1019133611148

Predicting Aqueous Free Energies of Solvation as Functions of Temperature
journal, March 2006

  • Chamberlin, Adam C.; Cramer, Christopher J.; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 11
  • DOI: 10.1021/jp057264y

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations
journal, March 2015

  • Anandakrishnan, Ramu; Drozdetski, Aleksander; Walker, Ross C.
  • Biophysical Journal, Vol. 108, Issue 5
  • DOI: 10.1016/j.bpj.2014.12.047

Reevaluation of the Born model of ion hydration
journal, December 1985

  • Rashin, Alexander A.; Honig, Barry
  • The Journal of Physical Chemistry, Vol. 89, Issue 26
  • DOI: 10.1021/j100272a006

The role of Stern layer in the interplay of dielectric saturation and ion steric effects for the capacitance of graphene in aqueous electrolytes
journal, March 2017

  • Daniels, Lindsey; Scott, Matthew; Mišković, Z. L.
  • The Journal of Chemical Physics, Vol. 146, Issue 9
  • DOI: 10.1063/1.4976991

New Model for Calculation of Solvation Free Energies:  Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects
journal, January 1996

  • Marten, Bryan; Kim, Kyungsun; Cortis, Christian
  • The Journal of Physical Chemistry, Vol. 100, Issue 28
  • DOI: 10.1021/jp953087x

Macromolecular electrostatic energy within the nonlinear Poisson–Boltzmann equation
journal, February 1994

  • Zhou, Huan‐Xiang
  • The Journal of Chemical Physics, Vol. 100, Issue 4
  • DOI: 10.1063/1.466406

Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model
journal, November 1999

  • Florián, Jan; Warshel, Arieh
  • The Journal of Physical Chemistry B, Vol. 103, Issue 46
  • DOI: 10.1021/jp992041r

Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations
journal, January 2009

  • Mobley, David L.; Bayly, Christopher I.; Cooper, Matthew D.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 2
  • DOI: 10.1021/ct800409d

The Many Roles of Computation in Drug Discovery
journal, March 2004

Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations
journal, February 1991

  • Jean-Charles, Arald; Nicholls, Anthony; Sharp, Kim
  • Journal of the American Chemical Society, Vol. 113, Issue 4
  • DOI: 10.1021/ja00004a079

Macroscopic models of aqueous solutions: biological and chemical applications
journal, February 1993

  • Honig, Barry; Sharp, Kim; Yang, An Suei
  • The Journal of Physical Chemistry, Vol. 97, Issue 6
  • DOI: 10.1021/j100108a002

Contribution of Hydration to Protein Folding Thermodynamics
journal, July 1993

  • Makhatadze, George I.; Privalov, Peter L.
  • Journal of Molecular Biology, Vol. 232, Issue 2
  • DOI: 10.1006/jmbi.1993.1416

Analytical molecular surface calculation
journal, October 1983

Derivative-free optimization for parameter estimation in computational nuclear physics
journal, February 2015

  • Wild, Stefan M.; Sarich, Jason; Schunck, Nicolas
  • Journal of Physics G: Nuclear and Particle Physics, Vol. 42, Issue 3
  • DOI: 10.1088/0954-3899/42/3/034031

Modeling opto-electronic properties of a dye molecule in proximity of a semiconductor nanoparticle
journal, July 2013

  • Delgado, Alain; Corni, Stefano; Goldoni, Guido
  • The Journal of Chemical Physics, Vol. 139, Issue 2
  • DOI: 10.1063/1.4812680

The statistical-thermodynamic basis for computation of binding affinities: a critical review
journal, March 1997

Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?
journal, October 2007

  • Cerutti, David S.; Baker, Nathan A.; McCammon, J. Andrew
  • The Journal of Chemical Physics, Vol. 127, Issue 15
  • DOI: 10.1063/1.2771171

Continuous surface charge polarizable continuum models of solvation. I. General formalism
journal, March 2010

  • Scalmani, Giovanni; Frisch, Michael J.
  • The Journal of Chemical Physics, Vol. 132, Issue 11
  • DOI: 10.1063/1.3359469

Free energies of solvation in the context of protein folding: Implications for implicit and explicit solvent models
journal, November 2015

  • Cumberworth, Alexander; Bui, Jennifer M.; Gsponer, Jörg
  • Journal of Computational Chemistry, Vol. 37, Issue 7
  • DOI: 10.1002/jcc.24235

A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
journal, August 1997

  • Cancès, E.; Mennucci, B.; Tomasi, J.
  • The Journal of Chemical Physics, Vol. 107, Issue 8
  • DOI: 10.1063/1.474659

Extension of a Temperature-Dependent Aqueous Solvation Model to Compounds Containing Nitrogen, Fluorine, Chlorine, Bromine, and Sulfur
journal, March 2008

  • Chamberlin, Adam C.; Cramer, Christopher J.; Truhlar, Donald G.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 10
  • DOI: 10.1021/jp076682v

Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
journal, February 1994

  • Sitkoff, Doree; Sharp, Kim A.; Honig, Barry
  • The Journal of Physical Chemistry, Vol. 98, Issue 7
  • DOI: 10.1021/j100058a043

Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions
journal, October 2014

  • Bardhan, Jaydeep P.; Knepley, Matthew G.
  • The Journal of Chemical Physics, Vol. 141, Issue 13
  • DOI: 10.1063/1.4897324

Continuum Solvation Models: What Else Can We Learn from Them?
journal, April 2010

  • Mennucci, Benedetta
  • The Journal of Physical Chemistry Letters, Vol. 1, Issue 10
  • DOI: 10.1021/jz100506s

On the calculation of electrostatic interactions in proteins
journal, August 1985

Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations †
journal, April 2009

  • Mobley, David L.; Bayly, Christopher I.; Cooper, Matthew D.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 14
  • DOI: 10.1021/jp806838b

Convergence of Molecular and Macroscopic Continuum Descriptions of Ion Hydration
journal, August 2000

  • Ashbaugh, Henry S.
  • The Journal of Physical Chemistry B, Vol. 104, Issue 31
  • DOI: 10.1021/jp0015067

On the Validity of Electrostatic Linear Response in Polar Solvents
journal, January 1996

  • Åqvist, Johan; Hansson, Tomas
  • The Journal of Physical Chemistry, Vol. 100, Issue 22
  • DOI: 10.1021/jp953640a

FreeSolv: a database of experimental and calculated hydration free energies, with input files
journal, June 2014

  • Mobley, David L.; Guthrie, J. Peter
  • Journal of Computer-Aided Molecular Design, Vol. 28, Issue 7
  • DOI: 10.1007/s10822-014-9747-x

High-Throughput Prediction of the Hydration Free Energies of Small Molecules from a Classical Density Functional Theory
journal, October 2013

  • Liu, Yu; Fu, Jia; Wu, Jianzhong
  • The Journal of Physical Chemistry Letters, Vol. 4, Issue 21
  • DOI: 10.1021/jz401787p

Restoring Charge Asymmetry in Continuum Electrostatics Calculations of Hydration Free Energies
journal, June 2009

  • Purisima, Enrico O.; Sulea, Traian
  • The Journal of Physical Chemistry B, Vol. 113, Issue 24
  • DOI: 10.1021/jp9020799

A view of thermodynamics of hydration emerging from continuum studies
journal, August 1994

Communication: Accurate hydration free energies at a wide range of temperatures from 3D-RISM
journal, March 2015

  • Misin, Maksim; Fedorov, Maxim V.; Palmer, David S.
  • The Journal of Chemical Physics, Vol. 142, Issue 9
  • DOI: 10.1063/1.4914315

Continuum based calculations of hydration entropies and the hydrophobic effect
journal, April 1991

  • Rashin, Alexander A.; Bukatin, Michael A.
  • The Journal of Physical Chemistry, Vol. 95, Issue 8
  • DOI: 10.1021/j100161a002

Biomolecular electrostatics—I want your solvation (model)
journal, January 2012

A stringent test of the cavity concept in continuum dielectrics
journal, November 1997

  • Papazyan, Arno; Warshel, Arieh
  • The Journal of Chemical Physics, Vol. 107, Issue 19
  • DOI: 10.1063/1.475059

Charge penetration in dielectric models of solvation
journal, June 1997

  • Chipman, Daniel M.
  • The Journal of Chemical Physics, Vol. 106, Issue 24
  • DOI: 10.1063/1.474048

Domain decomposition for implicit solvation models
journal, August 2013

  • Cancès, Eric; Maday, Yvon; Stamm, Benjamin
  • The Journal of Chemical Physics, Vol. 139, Issue 5
  • DOI: 10.1063/1.4816767

Thermodynamics of Ion Hydration as a Measure of Effective Dielectric Properties of Water
journal, February 1962

  • Noyes, Richard M.
  • Journal of the American Chemical Society, Vol. 84, Issue 4
  • DOI: 10.1021/ja00863a002

Field-Extremum Model for Short-Range Contributions to Hydration Free Energy
journal, October 2011

  • Pomogaeva, Anna; Chipman, Daniel M.
  • Journal of Chemical Theory and Computation, Vol. 7, Issue 12
  • DOI: 10.1021/ct200575c

Protein Dielectric Constants Determined from NMR Chemical Shift Perturbations
journal, October 2013

  • Kukic, Predrag; Farrell, Damien; McIntosh, Lawrence P.
  • Journal of the American Chemical Society, Vol. 135, Issue 45
  • DOI: 10.1021/ja406995j

Hydration Thermodynamic Properties of Amino Acid Analogues:  A Systematic Comparison of Biomolecular Force Fields and Water Models
journal, September 2006

  • Hess, Berk; van der Vegt, Nico F. A.
  • The Journal of Physical Chemistry B, Vol. 110, Issue 35
  • DOI: 10.1021/jp0641029

Hydration Energy from a Composite Method for Implicit Representation of Solvent
journal, November 2013

  • Pomogaeva, Anna; Chipman, Daniel M.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 1
  • DOI: 10.1021/ct400894j

Composite Method for Implicit Representation of Solvent in Dimethyl Sulfoxide and Acetonitrile
journal, December 2014

  • Pomogaeva, Anna; Chipman, Daniel M.
  • The Journal of Physical Chemistry A, Vol. 119, Issue 21
  • DOI: 10.1021/jp5098519

Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms
journal, May 2006

  • Wagoner, J. A.; Baker, N. A.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 22
  • DOI: 10.1073/pnas.0600118103

Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies
journal, September 2012

  • Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee
  • The Journal of Chemical Physics, Vol. 137, Issue 12
  • DOI: 10.1063/1.4752735

Implicit solvent models
journal, April 1999

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson–Boltzmann Solvent
journal, May 2017

  • Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali
  • Journal of Chemical Theory and Computation, Vol. 13, Issue 6
  • DOI: 10.1021/acs.jctc.6b00832

Introducing Charge Hydration Asymmetry into the Generalized Born Model
journal, March 2014

  • Mukhopadhyay, Abhishek; Aguilar, Boris H.; Tolokh, Igor S.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 4
  • DOI: 10.1021/ct4010917

Dielectric response of the water hydration layer around spherical solutes
journal, September 2015

Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution
journal, August 1981

  • Cabani, Sergio; Gianni, Paolo; Mollica, Vincenzo
  • Journal of Solution Chemistry, Vol. 10, Issue 8
  • DOI: 10.1007/BF00646936

The AGBNP2 Implicit Solvation Model
journal, July 2009

  • Gallicchio, Emilio; Paris, Kristina; Levy, Ronald M.
  • Journal of Chemical Theory and Computation, Vol. 5, Issue 9
  • DOI: 10.1021/ct900234u

Free energy calculations: Applications to chemical and biochemical phenomena
journal, November 1993

    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: