Comparison of two simulation methods to compute solvation free energies and partition coefficients

Yang, Li; Ahmed, Alauddin; Sandler, Stanley I.

doi:10.1002/jcc.23127

Title: Comparison of two simulation methods to compute solvation free energies and partition coefficients

Journal Article · Mon Oct 29 00:00:00 EDT 2012 · Journal of Computational Chemistry

DOI:https://doi.org/10.1002/jcc.23127· OSTI ID:1382193

Yang, Li; Ahmed, Alauddin; Sandler, Stanley I.

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Research Organization:: Energy Frontier Research Centers (EFRC) (United States). Catalysis Center for Energy Innovation (CCEI)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

DOE Contract Number:: SC0001004

OSTI ID:: 1382193

Journal Information:: Journal of Computational Chemistry, Vol. 34, Issue 4; Related Information: CCEI partners with the University of Delaware (lead); Brookhaven National Laboratory; California Institute of Technology; Columbia University; University of Delaware; Lehigh University; University of Massachusetts, Amherst; Massachusetts Institute of Technology; University of Minnesota; Pacific Northwest National Laboratory; University of Pennsylvania; Princeton University; Rutgers University; ISSN 0192-8651

Publisher:: Wiley

Country of Publication:: United States

Language:: English

References (56)

Charge Asymmetries in Hydration of Polar Solutes Mobley, David L.; Barber, Alan E.; Fennell, Christopher J. The Journal of Physical Chemistry B, Vol. 112, Issue 8 https://doi.org/10.1021/jp709958f	journal	February 2008
Prediction of the n -hexane/water and 1-octanol/water partition coefficients for environmentally relevant compounds using molecular simulation Garrido, Nuno M.; Economou, Ioannis G.; Queimada, António J. AIChE Journal, Vol. 58, Issue 6 https://doi.org/10.1002/aic.12718	journal	August 2011
Alcohol Adsorption onto Silicalite from Aqueous Solution Xiong, Ruichang; Sandler, Stanley I.; Vlachos, Dionisios G. The Journal of Physical Chemistry C, Vol. 115, Issue 38 https://doi.org/10.1021/jp205312k	journal	September 2011
Molecular dynamics on hypercube parallel computers Smith, W. Computer Physics Communications, Vol. 62, Issue 2-3, p. 229-248 https://doi.org/10.1016/0010-4655(91)90097-5	journal	March 1991
Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent Mobley, David L.; Dumont, Élise; Chodera, John D. The Journal of Physical Chemistry B, Vol. 111, Issue 9 https://doi.org/10.1021/jp0667442	journal	March 2007
Engineering a Molecular Model for Water Phase Equilibrium over a Wide Temperature Range Boulougouris, Georgios C.; Economou, Ioannis G.; Theodorou, Doros N. The Journal of Physical Chemistry B, Vol. 102, Issue 6 https://doi.org/10.1021/jp972582l	journal	February 1998
Scalable molecular dynamics with NAMD Phillips, James C.; Braun, Rosemary; Wang, Wei Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802 https://doi.org/10.1002/jcc.20289	journal	January 2005
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation Hess, Berk; Kutzner, Carsten; van der Spoel, David Journal of Chemical Theory and Computation, Vol. 4, Issue 3 https://doi.org/10.1021/ct700301q	journal	February 2008
Comparison of free energy methods for molecular systems Ytreberg, F. Marty; Swendsen, Robert H.; Zuckerman, Daniel M. The Journal of Chemical Physics, Vol. 125, Issue 18 https://doi.org/10.1063/1.2378907	journal	November 2006
A new Measure of rank Correlation Kendall, M. G. Biometrika, Vol. 30, Issue 1-2 https://doi.org/10.1093/biomet/30.1-2.81	journal	June 1938
Efficient estimation of free energy differences from Monte Carlo data Bennett, Charles H. Journal of Computational Physics, Vol. 22, Issue 2 https://doi.org/10.1016/0021-9991(76)90078-4	journal	October 1976
Novel Configurational-Bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-Atom Description of Branched Alkanes Martin, Marcus G.; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 103, Issue 21 https://doi.org/10.1021/jp984742e	journal	May 1999
Phase-space overlap measures. II. Design and implementation of staging methods for free-energy calculations Wu, Di; Kofke, David A. The Journal of Chemical Physics, Vol. 123, Issue 8 https://doi.org/10.1063/1.2011391	journal	August 2005
Solvation Free Energy of Amino Acids and Side-Chain Analogues Chang, Jaeeon; Lenhoff, Abraham M.; Sandler, Stanley I. The Journal of Physical Chemistry B, Vol. 111, Issue 8 https://doi.org/10.1021/jp0620163	journal	February 2007
GROMACS: Fast, flexible, and free Van Der Spoel, David; Lindahl, Erik; Hess, Berk Journal of Computational Chemistry, Vol. 26, Issue 16 https://doi.org/10.1002/jcc.20291	journal	January 2005
Predicting the Solubility of the Sparingly Soluble Solids 1,2,4,5-Tetramethylbenzene, Phenanthrene, and Fluorene in Various Organic Solvents by Molecular Simulation Paluch, Andrew S.; Cryan, Dan D.; Maginn, Edward J. Journal of Chemical & Engineering Data, Vol. 56, Issue 4 https://doi.org/10.1021/je101251n	journal	March 2011
Structural Evidence for the Ordered Crystallites of Ionic Liquid in Confined Carbon Nanotubes Dong, Kun; Zhou, Guohui; Liu, Xiaomin The Journal of Physical Chemistry C, Vol. 113, Issue 23 https://doi.org/10.1021/jp900533k	journal	May 2009
Fast Parallel Algorithms for Short-Range Molecular Dynamics Plimpton, Steve Journal of Computational Physics, Vol. 117, Issue 1 https://doi.org/10.1006/jcph.1995.1039	journal	March 1995
Assessing equilibration and convergence in biomolecular simulations Smith, Lorna J.; Daura, Xavier; van Gunsteren, Wilfred F. Proteins: Structure, Function, and Genetics, Vol. 48, Issue 3 https://doi.org/10.1002/prot.10144	journal	June 2002
A Leap-frog Algorithm for Stochastic Dynamics Van Gunsteren, W. F.; Berendsen, H. J. C. Molecular Simulation, Vol. 1, Issue 3 https://doi.org/10.1080/08927028808080941	journal	March 1988
Reversible multiple time scale molecular dynamics Tuckerman, M.; Berne, B. J.; Martyna, G. J. The Journal of Chemical Physics, Vol. 97, Issue 3 https://doi.org/10.1063/1.463137	journal	August 1992
Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes Martin, Marcus G.; Siepmann, J. Ilja https://doi.org/10.1021/jp972543+		March 1998
Calculating the free energy of self-assembled structures by thermodynamic integration Müller, Marcus; Daoulas, Kostas Ch. The Journal of Chemical Physics, Vol. 128, Issue 2 https://doi.org/10.1063/1.2818565	journal	January 2008
Similarities between principal components of protein dynamics and random diffusion Hess, Berk Physical Review E, Vol. 62, Issue 6 https://doi.org/10.1103/PhysRevE.62.8438	journal	December 2000
Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible? Knapp, B.; Frantal, S.; Cibena, M. Journal of Computational Biology, Vol. 18, Issue 8 https://doi.org/10.1089/cmb.2010.0237	journal	August 2011
Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States Wang, Fugao; Landau, D. P. Physical Review Letters, Vol. 86, Issue 10 https://doi.org/10.1103/PhysRevLett.86.2050	journal	March 2001
DL_POLY: Application to molecular simulation Smith, W.; Yong, C. W.; Rodger, P. M. Molecular Simulation, Vol. 28, Issue 5 https://doi.org/10.1080/08927020290018769	journal	May 2002
Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry Nicholls, Anthony; Mobley, David L.; Guthrie, J. Peter Journal of Medicinal Chemistry, Vol. 51, Issue 4 https://doi.org/10.1021/jm070549+	journal	January 2008
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations Beutler, Thomas C.; Mark, Alan E.; van Schaik, René C. Chemical Physics Letters, Vol. 222, Issue 6 https://doi.org/10.1016/0009-2614(94)00397-1	journal	June 1994
Solvation free energies of amino acid side chain analogs for common molecular mechanics water models Shirts, Michael R.; Pande, Vijay S. The Journal of Chemical Physics, Vol. 122, Issue 13 https://doi.org/10.1063/1.1877132	journal	April 2005
Chapter 2 Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations Grossfield, Alan; Zuckerman, Daniel M. https://doi.org/10.1016/S1574-1400(09)00502-7	book	January 2009
Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration Bruckner, Stefan; Boresch, Stefan Journal of Computational Chemistry, Vol. 32, Issue 7 https://doi.org/10.1002/jcc.21712	journal	December 2010
Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method Bruckner, Stefan; Boresch, Stefan Journal of Computational Chemistry, Vol. 32, Issue 7 https://doi.org/10.1002/jcc.21713	journal	December 2010
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids Jorgensen, William L.; Maxwell, David S.; Tirado-Rives, Julian Journal of the American Chemical Society, Vol. 118, Issue 45 https://doi.org/10.1021/ja9621760	journal	January 1996
Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation Paluch, Andrew S.; Mobley, David L.; Maginn, Edward J. Journal of Chemical Theory and Computation, Vol. 7, Issue 9 https://doi.org/10.1021/ct200377w	journal	July 2011
New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V. The Journal of Chemical Physics, Vol. 96, Issue 3 https://doi.org/10.1063/1.462133	journal	February 1992
Free energy calculations by computer simulation Bash, P.; Singh, U.; Langridge, R. Science, Vol. 236, Issue 4801 https://doi.org/10.1126/science.3576184	journal	May 1987
Thermodynamics of solute transfer from water to hexadecane Abraham, Michael H.; Whiting, Gary S.; Fuchs, Richard Journal of the Chemical Society, Perkin Transactions 2, Issue 2 https://doi.org/10.1039/p29900000291	journal	January 1990
Molecular dynamics with coupling to an external bath Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F. The Journal of Chemical Physics, Vol. 81, Issue 8 https://doi.org/10.1063/1.448118	journal	October 1984
Solvation thermodynamics of nonionic solutes Ben‐Naim, A.; Marcus, Y. The Journal of Chemical Physics, Vol. 81, Issue 4 https://doi.org/10.1063/1.447824	journal	August 1984
Transferable Potentials for Phase Equilibria. 9. Explicit Hydrogen Description of Benzene and Five-Membered and Six-Membered Heterocyclic Aromatic Compounds Rai, Neeraj; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 111, Issue 36 https://doi.org/10.1021/jp073586l	journal	September 2007
Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins Shirts, Michael R.; Pitera, Jed W.; Swope, William C. The Journal of Chemical Physics, Vol. 119, Issue 11 https://doi.org/10.1063/1.1587119	journal	September 2003
Density-of-states Monte Carlo method for simulation of fluids Yan, Qiliang; Faller, Roland; de Pablo, Juan J. The Journal of Chemical Physics, Vol. 116, Issue 20 https://doi.org/10.1063/1.1463055	journal	May 2002
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems Jorgensen, W. L.; Tirado-Rives, J. Proceedings of the National Academy of Sciences, Vol. 102, Issue 19 https://doi.org/10.1073/pnas.0408037102	journal	May 2005
Alchemical prediction of hydration free energies for SAMPL Mobley, David L.; Liu, Shaui; Cerutti, David S. Journal of Computer-Aided Molecular Design, Vol. 26, Issue 5 https://doi.org/10.1007/s10822-011-9528-8	journal	December 2011
Statistically optimal analysis of samples from multiple equilibrium states Shirts, Michael R.; Chodera, John D. The Journal of Chemical Physics, Vol. 129, Issue 12 https://doi.org/10.1063/1.2978177	journal	September 2008
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models Miyamoto, Shuichi; Kollman, Peter A. Journal of Computational Chemistry, Vol. 13, Issue 8 https://doi.org/10.1002/jcc.540130805	journal	October 1992
Determination of solvation free energies by adaptive expanded ensemble molecular dynamics Åberg, K. Magnus; Lyubartsev, Alexander P.; Jacobsson, Sven P. The Journal of Chemical Physics, Vol. 120, Issue 8 https://doi.org/10.1063/1.1642601	journal	February 2004
Monte Carlo Calculations for Alcohols and Their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-Atom Description of Primary, Secondary, and Tertiary Alcohols Chen, Bin; Potoff, Jeffrey J.; Siepmann, J. Ilja The Journal of Physical Chemistry B, Vol. 105, Issue 15 https://doi.org/10.1021/jp003882x	journal	April 2001
Solubility of Organic Compounds in Water/Octanol Systems. A Expanded Ensemble Molecular Dynamics Simulation Study of log P Parameters Lyubartsev, Alexander P.; Jacobsson, Sven P.; Sundholm, Göran The Journal of Physical Chemistry B, Vol. 105, Issue 32 https://doi.org/10.1021/jp0036902	journal	August 2001
The missing term in effective pair potentials Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Journal of Physical Chemistry, Vol. 91, Issue 24 https://doi.org/10.1021/j100308a038	journal	November 1987
1-Octanol/Water Partition Coefficients of n -Alkanes from Molecular Simulations of Absolute Solvation Free Energies Garrido, Nuno M.; Queimada, António J.; Jorge, Miguel Journal of Chemical Theory and Computation, Vol. 5, Issue 9 https://doi.org/10.1021/ct900214y	journal	August 2009
Optimization of expanded ensemble methods Escobedo, Fernando A.; Martinez-Veracoechea, Francisco J. The Journal of Chemical Physics, Vol. 129, Issue 15 https://doi.org/10.1063/1.2994717	journal	October 2008
Relative partition coefficients for organic solutes from fluid simulations Jorgensen, William L.; Briggs, James M.; Contreras, M. Leonor. The Journal of Physical Chemistry, Vol. 94, Issue 4 https://doi.org/10.1021/j100367a084	journal	February 1990
Statistical Mechanics of Fluid Mixtures Kirkwood, John G. The Journal of Chemical Physics, Vol. 3, Issue 5 https://doi.org/10.1063/1.1749657	journal	May 1935
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems Beveridge, D. L.; DiCapua, F. M. Annual Review of Biophysics and Biophysical Chemistry, Vol. 18, Issue 1 https://doi.org/10.1146/annurev.bb.18.060189.002243	journal	June 1989

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Title: Comparison of two simulation methods to compute solvation free energies and partition coefficients

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