1
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Fowles DJ, Palmer DS. Solvation entropy, enthalpy and free energy prediction using a multi-task deep learning functional in 1D-RISM. Phys Chem Chem Phys 2023; 25:6944-6954. [PMID: 36806875 DOI: 10.1039/d3cp00199g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Simultaneous calculation of entropies, enthalpies and free energies has been a long-standing challenge in computational chemistry, partly because of the difficulty in obtaining estimates of all three properties from a single consistent simulation methodology. This has been particularly true for methods from the Integral Equation Theory of Molecular Liquids such as the Reference Interaction Site Model which have traditionally given large errors in solvation thermodynamics. Recently, we presented pyRISM-CNN, a combination of the 1 Dimensional Reference Interaction Site Model (1D-RISM) solver, pyRISM, with a deep learning based free energy functional, as a method of predicting solvation free energy (SFE). With this approach, a 40-fold improvement in prediction accuracy was delivered for a multi-solvent, multi-temperature dataset when compared to the standard 1D-RISM theory [Fowles et al., Digital Discovery, 2023, 2, 177-188]. Here, we report three further developments to the pyRISM-CNN methodology. Firstly, solvation free energies have been introduced for organic molecular ions in methanol or water solvent systems at 298 K, with errors below 4 kcal mol-1 obtained without the need for corrections or additional descriptors. Secondly, the number of solvents in the training data has been expanded from carbon tetrachloride, water and chloroform to now also include methanol. For neutral solutes, prediction errors nearing or below 1 kcal mol-1 are obtained for each organic solvent system at 298 K and water solvent systems at 273-373 K. Lastly, pyRISM-CNN was successfully applied to the simultaneous prediction of solvation enthalpy, entropy and free energy through a multi-task learning approach, with errors of 1.04, 0.98 and 0.47 kcal mol-1, respectively, for water solvent systems at 298 K.
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Affiliation(s)
- Daniel J Fowles
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK.
| | - David S Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK.
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2
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Raposo DJ. Effect of Conformational Equilibrium on Solvation Properties of 1,2-DCE in Water: A Solvation Thermodynamics and 3D-RISM Study. J Phys Chem B 2023; 127:757-765. [PMID: 36626710 DOI: 10.1021/acs.jpcb.2c07836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The contributions of the enthalpy and entropy of solvation for the study of chemical and biological systems are important in the prediction, interpretation, and manipulation of these processes. The relation between solvation Gibbs energies, enthalpies, and entropies of solvation, and their rigorous relation with the conformational equilibrium, are derived for the first time and applied with a computational method, in accordance with the Solvation Thermodynamics previous results, to 1,2-dichloroethane solvation in water. The rigid conformer calculations in solution were performed by using PC+/3D-RISM approach, with the conformational averaged results for enthalpy and solvation Gibbs energy reproducing the experimental results quite successfully. A qualitative agreement in the entropy of solvation predictions was also observed.
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Affiliation(s)
- Diego J Raposo
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco50740-560, Brazil
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3
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Ding L, Levesque M, Borgis D, Belloni L. Efficient molecular density functional theory using generalized spherical harmonics expansions. J Chem Phys 2017; 147:094107. [DOI: 10.1063/1.4994281] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lu Ding
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École Normale Supérieure, CNRS, Processus d’Activation Sélective par Transfert d’Énergie Uni-Électronique ou Radiatif (PASTEUR), 75005 Paris, France
| | - Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École Normale Supérieure, CNRS, Processus d’Activation Sélective par Transfert d’Énergie Uni-Électronique ou Radiatif (PASTEUR), 75005 Paris, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
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4
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Palmer DS, Mišin M, Fedorov MV, Llinas A. Fast and General Method To Predict the Physicochemical Properties of Druglike Molecules Using the Integral Equation Theory of Molecular Liquids. Mol Pharm 2015. [PMID: 26212723 DOI: 10.1021/acs.molpharmaceut.5b00441] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a method to predict physicochemical properties of druglike molecules using a classical statistical mechanics based solvent model combined with machine learning. The RISM-MOL-INF method introduced here provides an accurate technique to characterize solvation and desolvation processes based on solute-solvent correlation functions computed by the 1D reference interaction site model of the integral equation theory of molecular liquids. These functions can be obtained in a matter of minutes for most small organic and druglike molecules using existing software (RISM-MOL) (Sergiievskyi, V. P.; Hackbusch, W.; Fedorov, M. V. J. Comput. Chem. 2011, 32, 1982-1992). Predictions of caco-2 cell permeability and hydration free energy obtained using the RISM-MOL-INF method are shown to be more accurate than the state-of-the-art tools for benchmark data sets. Due to the importance of solvation and desolvation effects in biological systems, it is anticipated that the RISM-MOL-INF approach will find many applications in biophysical and biomedical property prediction.
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Affiliation(s)
- David S Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde , Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - Maksim Mišin
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, U.K
| | - Maxim V Fedorov
- Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, U.K
| | - Antonio Llinas
- Respiratory, Inflammation and Autoimmune iMed, AstraZeneca R&D , Pepparedsleden 1, SE-431 83, Mölndal, Sweden
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5
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Ratkova EL, Palmer DS, Fedorov MV. Solvation thermodynamics of organic molecules by the molecular integral equation theory: approaching chemical accuracy. Chem Rev 2015; 115:6312-56. [PMID: 26073187 DOI: 10.1021/cr5000283] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Ekaterina L Ratkova
- †G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia.,‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - David S Palmer
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,§Department of Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, United Kingdom
| | - Maxim V Fedorov
- ‡The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany.,∥Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow East, Glasgow G4 0NG, United Kingdom
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6
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Sergiievskyi VP, Jeanmairet G, Levesque M, Borgis D. Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections. J Phys Chem Lett 2014; 5:1935-1942. [PMID: 26273876 DOI: 10.1021/jz500428s] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.
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Affiliation(s)
- Volodymyr P Sergiievskyi
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Guillaume Jeanmairet
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Maximilien Levesque
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Daniel Borgis
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
- ‡Maison de la Simulation, CNRS USR 3441, CEA Saclay, 91191 Gif-sur-Yvette, France
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7
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Chuev GN, Vyalov I, Georgi N. Extraction of site-site bridge functions and effective pair potentials from simulations of polar molecular liquids. J Comput Chem 2014; 35:1010-23. [DOI: 10.1002/jcc.23586] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 02/08/2014] [Accepted: 02/13/2014] [Indexed: 01/13/2023]
Affiliation(s)
- Gennady N. Chuev
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science; Pushchino Moscow Region 142290 Russia
| | - Ivan Vyalov
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
| | - Nikolaj Georgi
- Max Planck Institute for Mathematics in the Sciences; Inselstrasse 22 Leipzig 04103 Germany
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8
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Palmer DS, Sørensen J, Schiøtt B, Fedorov MV. Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin–Bovine κ-Casein Complex Using Molecular Integral Equation Theory. J Chem Theory Comput 2013; 9:5706-17. [DOI: 10.1021/ct400605x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Palmer
- Department
of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Jesper Sørensen
- Department
of Chemistry and Biochemistry, University of California, San Diego, Urey Hall, 9500 Gilman Drive, La Jolla, California 92093, United States
- The
Center for Insoluble Protein Structures (inSPIN) and the Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Birgit Schiøtt
- The
Center for Insoluble Protein Structures (inSPIN) and the Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Maxim V. Fedorov
- Department
of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
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9
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Palmer DS, McDonagh JL, Mitchell JBO, van Mourik T, Fedorov MV. First-Principles Calculation of the Intrinsic Aqueous Solubility of Crystalline Druglike Molecules. J Chem Theory Comput 2012; 8:3322-37. [PMID: 26605739 DOI: 10.1021/ct300345m] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We demonstrate that the intrinsic aqueous solubility of crystalline druglike molecules can be estimated with reasonable accuracy from sublimation free energies calculated using crystal lattice simulations and hydration free energies calculated using the 3D Reference Interaction Site Model (3D-RISM) of the Integral Equation Theory of Molecular Liquids (IET). The solubilities of 25 crystalline druglike molecules taken from different chemical classes are predicted by the model with a correlation coefficient of R = 0.85 and a root mean square error (RMSE) equal to 1.45 log10S units, which is significantly more accurate than results obtained using implicit continuum solvent models. The method is not directly parametrized against experimental solubility data, and it offers a full computational characterization of the thermodynamics of transfer of the drug molecule from crystal phase to gas phase to dilute aqueous solution.
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Affiliation(s)
- David S Palmer
- Department of Physics, University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom.,Max Planck Institute for Mathematics in the Sciences , Inselstrasse 22, DE-04103 Leipzig, Germany
| | - James L McDonagh
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - John B O Mitchell
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - Tanja van Mourik
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St. Andrews , Purdie Building, North Haugh, St. Andrews, Scotland KY16 9ST, United Kingdom
| | - Maxim V Fedorov
- Department of Physics, University of Strathclyde , John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom.,Max Planck Institute for Mathematics in the Sciences , Inselstrasse 22, DE-04103 Leipzig, Germany
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10
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Sergiievskyi VP, Frolov AI. A universal bridge functional for infinitely diluted solutions: A case study for Lennard-Jones spheres of different diameters. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412080122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Sergiievskyi VP, Fedorov MV. 3DRISM Multigrid Algorithm for Fast Solvation Free Energy Calculations. J Chem Theory Comput 2012; 8:2062-70. [DOI: 10.1021/ct200815v] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Maxim V. Fedorov
- Nanoscience
Division, Department
of Physics, Scottish Universities Physics Alliance (SUPA), Strathclyde University, Room JA 6.10, John Anderson
Building 107, Rottenrow East Glasgow, United Kingdom G4 0NG
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12
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Luchko T, Joung IS, Case DA. Integral Equation Theory of Biomolecules and Electrolytes. INNOVATIONS IN BIOMOLECULAR MODELING AND SIMULATIONS 2012. [DOI: 10.1039/9781849735049-00051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The so-called three-dimensional version (3D-RISM) can be used to describe the interactions of solvent components (here we treat water and ions) with a chemical or biomolecular solute of arbitrary size and shape. Here we give an overview of the current status of such models, describing some aspects of “pure” electrolytes (water plus simple ions) and of ionophores, proteins and nucleic acids in the presence of water and salts. Here we focus primarily on interactions with water and dissolved salts; as a practical matter, the discussion is mostly limited to monovalent ions, since studies of divalent ions present many difficult problems that have not yet been addressed. This is not a comprehensive review, but covers a few recent examples that illustrate current issues.
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Affiliation(s)
- Tyler Luchko
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
| | - In Suk Joung
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
| | - David A. Case
- Department of Chemistry and Chemical Biology and BioMaPS Institute Rutgers University Piscataway NJ 08854, USA
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13
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Chuev GN, Valiev M, Fedotova MV. Integral Equation Theory of Molecular Solvation Coupled with Quantum Mechanical/Molecular Mechanics Method in NWChem Package. J Chem Theory Comput 2012; 8:1246-54. [DOI: 10.1021/ct2009297] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gennady N. Chuev
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig,
04103, Germany
- Institute
of Theoretical and
Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Marat Valiev
- William R. Wiley Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P. O. Box 999, Richland, Washington 99352,
United States
| | - Marina V. Fedotova
- Institute
of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya Street, 1, 153045 Ivanovo, Russia
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Palmer DS, Frolov AI, Ratkova EL, Fedorov MV. Toward a Universal Model To Calculate the Solvation Thermodynamics of Druglike Molecules: The Importance of New Experimental Databases. Mol Pharm 2011; 8:1423-9. [DOI: 10.1021/mp200119r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Palmer
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Andrey I. Frolov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Ekaterina L. Ratkova
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Maxim V. Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
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15
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Ratkova EL, Fedorov MV. Combination of RISM and Cheminformatics for Efficient Predictions of Hydration Free Energy of Polyfragment Molecules: Application to a Set of Organic Pollutants. J Chem Theory Comput 2011; 7:1450-7. [DOI: 10.1021/ct100654h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ekaterina L. Ratkova
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
| | - Maxim V. Fedorov
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
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Frolov AI, Ratkova EL, Palmer DS, Fedorov MV. Hydration Thermodynamics Using the Reference Interaction Site Model: Speed or Accuracy? J Phys Chem B 2011; 115:6011-22. [DOI: 10.1021/jp111271c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Andrey I. Frolov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
| | - Ekaterina L. Ratkova
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
| | - David S. Palmer
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
| | - Maxim V. Fedorov
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
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