1
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Maruyama Y, Yoshida N. RISMiCal: A software package to perform fast RISM/3D-RISM calculations. J Comput Chem 2024; 45:1470-1482. [PMID: 38472097 DOI: 10.1002/jcc.27340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.
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Affiliation(s)
- Yutaka Maruyama
- Data Science Center for Creative Design and Manufacturing, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki-shi, Kanagawa, Japan
| | - Norio Yoshida
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Japan
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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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Roy D, Kovalenko A. A 3D-RISM-KH study of liquid nitromethane, nitroethane, and nitrobenzene as solvents. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Omelyan I, Kovalenko A. Enhanced solvation force extrapolation for speeding up molecular dynamics simulations of complex biochemical liquids. J Chem Phys 2019; 151:214102. [PMID: 31822083 DOI: 10.1063/1.5126410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We propose an enhanced approach to the extrapolation of mean potential forces acting on atoms of solute macromolecules due to their interactions with solvent atoms in complex biochemical liquids. It improves and extends our previous extrapolation schemes by additionally including new techniques such as an exponential scaling transformation of coordinate space with weights complemented by an automatically adjusted balancing between the least square minimization of force deviations and the norm of expansion coefficients in the approximation. The expensive mean potential forces are treated in terms of the three-dimensional reference interaction site model with Kovalenko-Hirata closure molecular theory of solvation. During the dynamics, they are calculated only after every long (outer) time interval, i.e., quite rarely to reduce the computational costs. At much shorter (inner) time steps, these forces are extrapolated on the basis of their outer values. The equations of motion are then solved using a multiple time step integration within an optimized isokinetic Nosé-Hoover chain thermostat. The new approach is applied to molecular dynamics simulations of various systems consisting of solvated organic and biomolecules of different complexity. For example, we consider hydrated alanine dipeptide, asphaltene in toluene solvent, miniprotein 1L2Y, and protein G in aqueous solution. It is shown that in all these cases, the enhanced extrapolation provides much better accuracy of the solvation force approximation than the existing approaches. As a result, it can be used with much larger outer time steps, leading to a significant speedup of the simulations.
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Affiliation(s)
- Igor Omelyan
- Institute for Condensed Matter Physics, National Academy of Sciences of Ukraine, 1 Svientsitskii Street, Lviv 79011, Ukraine
| | - Andriy Kovalenko
- Department of Mechanical Engineering, University of Alberta, 9211-116 Street NW, Edmonton, Alberta T6G 1H9, Canada
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Maruyama Y, Takano H, Mitsutake A. Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory. Biophys Physicobiol 2019; 16:407-429. [PMID: 31984194 PMCID: PMC6975981 DOI: 10.2142/biophysico.16.0_407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/29/2019] [Indexed: 01/03/2023] Open
Abstract
Molecular dynamics simulation is a fruitful tool for investigating the structural stability, dynamics, and functions of biopolymers at an atomic level. In recent years, simulations can be performed on time scales of the order of milliseconds using special purpose systems. Since the most stable structure, as well as meta-stable structures and intermediate structures, is included in trajectories in long simulations, it is necessary to develop analysis methods for extracting them from trajectories of simulations. For these structures, methods for evaluating the stabilities, including the solvent effect, are also needed. We have developed relaxation mode analysis to investigate dynamics and kinetics of simulations based on statistical mechanics. We have also applied the three-dimensional reference interaction site model theory to investigate stabilities with solvent effects. In this paper, we review the results for designing amino-acid substitution of the 10-residue peptide, chignolin, to stabilize the misfolded structure using these developed analysis methods.
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Affiliation(s)
- Yutaka Maruyama
- Architecture Development Team, FLAGSHIP 2020 Project, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Hiroshi Takano
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Ayori Mitsutake
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
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6
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Maruyama Y. Correction terms for the solvation free energy functional of three-dimensional reference interaction site model based on the reference-modified density functional theory. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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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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Chung KC, Park H. Accuracy enhancement in the estimation of molecular hydration free energies by implementing the intramolecular hydrogen bond effects. J Cheminform 2015; 7:57. [PMID: 26613005 PMCID: PMC4660792 DOI: 10.1186/s13321-015-0106-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 11/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background The formation of intramolecular hydrogen bonds (IHBs) may induce the remarkable changes in molecular physicochemical properties. Within the framework of the extended solvent-contact model, we investigate the effect of implementing the IHB interactions on the accuracy in estimating the molecular hydration free energies. Results The performances of hydration free energy functions including and excluding the IHB parameters are compared using the molecules distributed for SAMPL4 blind prediction challenge and those in Free Solvation Database (FSD). The calculated hydration free energies with IHB effects are found to be in considerably better agreement with the experimental data than those without them. For example, the root mean square error of the estimation decreases from 2.56 to 1.66 and from 1.73 to 1.54 kcal/mol for SAMPL4 and FSD molecules, respectively, due to the extension of atomic parameter space to cope with IHBs. Conclusions These improvements are made possible by reducing the overestimation of attractive interactions between water and the solute molecules involving IHBs. The modified hydration free energy function is thus anticipated to be useful for estimating the desolvation cost for various organic molecules. Electronic supplementary material The online version of this article (doi:10.1186/s13321-015-0106-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kee-Choo Chung
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 143-747 Republic of Korea
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul, 143-747 Republic of Korea
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Sergiievskyi V, Jeanmairet G, Levesque M, Borgis D. Solvation free-energy pressure corrections in the three dimensional reference interaction site model. J Chem Phys 2015; 143:184116. [DOI: 10.1063/1.4935065] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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10
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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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11
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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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12
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Abstract
The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.
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Affiliation(s)
- Jochen Heil
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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13
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Docherty R, Pencheva K, Abramov YA. Low solubility in drug development: de-convoluting the relative importance of solvation and crystal packing. ACTA ACUST UNITED AC 2015; 67:847-56. [PMID: 25880016 DOI: 10.1111/jphp.12393] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 01/06/2015] [Indexed: 12/12/2022]
Abstract
OBJECTIVES An increasing trend towards low solubility is a major issue for drug development as formulation of low solubility compounds can be problematic. This paper presents a model which de-convolutes the solubility of pharmaceutical compounds into solvation and packing properties with the intention to understand the solubility limiting features. METHODS The Cambridge Crystallographic Database was the source of structural information. Lattice energies were calculated via force-field based approaches using Materials Studio. The solvation energies were calculated applying quantum chemistry models using Cosmotherm software. KEY FINDINGS The solubilities of 54 drug-like compounds were mapped onto a solvation energy/crystal packing grid. Four quadrants were identified were different balances of solvation and packing were defining the solubility. A version of the model was developed which allows for the calculation of the two features even in absence of crystal structure. CONCLUSION Although there are significant number of in-silico models, it has been proven very difficult to predict aqueous solubility accurately. Therefore, we have taken a different approach where the solubility is not predicted directly but is de-convoluted into two constituent features.
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Affiliation(s)
- Robert Docherty
- Pharmaceutical Sciences, Pfizer Global R&D, Sandwich, Kent, UK
| | | | - Yuriy A Abramov
- Pharmaceutical Sciences, Pfizer Global R&D, Sandwich, Kent, UK
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14
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Misin M, Fedorov MV, Palmer DS. Communication: Accurate hydration free energies at a wide range of temperatures from 3D-RISM. J Chem Phys 2015; 142:091105. [DOI: 10.1063/1.4914315] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Maksim Misin
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - Maxim V. Fedorov
- Department of Physics, SUPA, University of Strathclyde, 107 Rottenrow, Glasgow G4 0NG, United Kingdom
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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15
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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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16
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Maruyama Y, Yoshida N, Tadano H, Takahashi D, Sato M, Hirata F. Massively parallel implementation of 3D-RISM calculation with volumetric 3D-FFT. J Comput Chem 2014; 35:1347-55. [PMID: 24771232 DOI: 10.1002/jcc.23619] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/26/2014] [Accepted: 04/06/2014] [Indexed: 01/19/2023]
Abstract
A new three-dimensional reference interaction site model (3D-RISM) program for massively parallel machines combined with the volumetric 3D fast Fourier transform (3D-FFT) was developed, and tested on the RIKEN K supercomputer. The ordinary parallel 3D-RISM program has a limitation on the number of parallelizations because of the limitations of the slab-type 3D-FFT. The volumetric 3D-FFT relieves this limitation drastically. We tested the 3D-RISM calculation on the large and fine calculation cell (2048(3) grid points) on 16,384 nodes, each having eight CPU cores. The new 3D-RISM program achieved excellent scalability to the parallelization, running on the RIKEN K supercomputer. As a benchmark application, we employed the program, combined with molecular dynamics simulation, to analyze the oligomerization process of chymotrypsin Inhibitor 2 mutant. The results demonstrate that the massive parallel 3D-RISM program is effective to analyze the hydration properties of the large biomolecular systems.
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Affiliation(s)
- Yutaka Maruyama
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, 223-8522, Japan
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17
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Extended solvent-contact model approach to SAMPL4 blind prediction challenge for hydration free energies. J Comput Aided Mol Des 2014; 28:175-86. [DOI: 10.1007/s10822-014-9729-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
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18
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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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Heinen M, Allahyarov E, Löwen H. Highly asymmetric electrolytes in the primitive model: Hypernetted chain solution in arbitrary spatial dimensions. J Comput Chem 2013; 35:275-89. [DOI: 10.1002/jcc.23446] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Marco Heinen
- Institut für Theoretische Physik II; Weiche Materie, Heinrich-Heine-Universität, Düsseldorf, 40225; Düsseldorf Germany
| | - Elshad Allahyarov
- Institut für Theoretische Physik II; Weiche Materie, Heinrich-Heine-Universität, Düsseldorf, 40225; Düsseldorf Germany
- Theoretical Department; Joint Institute for High Temperatures, Russian Academy of Sciences (IVTAN); 13/19 Izhorskaya street Moscow 125412 Russia
| | - Hartmut Löwen
- Institut für Theoretische Physik II; Weiche Materie, Heinrich-Heine-Universität, Düsseldorf, 40225; Düsseldorf Germany
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20
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Choi H, Kang H, Park H. New solvation free energy function comprising intermolecular solvation and intramolecular self-solvation terms. J Cheminform 2013; 5:8. [PMID: 23379425 PMCID: PMC3573996 DOI: 10.1186/1758-2946-5-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
Solvation free energy is a fundamental thermodynamic quantity that should be determined to estimate various physicochemical properties of a molecule and the desolvation cost for its binding to macromolecular receptors. Here, we propose a new solvation free energy function through the improvement of the solvent-contact model, and test its applicability in estimating the solvation free energies of organic molecules with varying sizes and shapes. This new solvation free energy function is constructed by combining the existing solute-solvent interaction term with the self-solvation term that reflects the effects of intramolecular interactions on solvation. Four kinds of atomic parameters should be determined in this solvation model: atomic fragmental volume, maximum atomic occupancy, atomic solvation, and atomic self-solvation parameters. All of these parameters for total 37 atom types are optimized by the operation of a standard genetic algorithm in such a way to minimize the difference between the experimental solvation free energies and those calculated by the solvation free energy function for 362 organic molecules. The solvation free energies estimated from the new solvation model compare well with the experimental results with the associated squared correlation coefficients of 0.88 and 0.85 for training and test sets, respectively. The present solvation model is thus expected to be useful for estimating the solvation free energies of organic molecules.
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Affiliation(s)
- Hwanho Choi
- Department of Bioscience and Biotechnology, Sejong University, 98 Kunja-dong, Kwangjin-ku, Seoul, 143-747, Korea.
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21
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Chong SH, Ham S. Aqueous interaction site integral-equation theory that exactly takes into account intramolecular correlations. J Chem Phys 2012; 137:154101. [DOI: 10.1063/1.4758072] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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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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