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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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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3
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Miyata T. Sigma enlarging bridge function for heteronuclear Lennard-Jones diatomic solute solvated in a Lennard-Jones monatomic solvent in terms of the parameter transferability. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Subramanian V, Ratkova E, Palmer D, Engkvist O, Fedorov M, Llinas A. Multisolvent Models for Solvation Free Energy Predictions Using 3D-RISM Hydration Thermodynamic Descriptors. J Chem Inf Model 2020; 60:2977-2988. [PMID: 32311268 DOI: 10.1021/acs.jcim.0c00065] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The potential to predict solvation free energies (SFEs) in any solvent using a machine learning (ML) model based on thermodynamic output, extracted exclusively from 3D-RISM simulations in water is investigated. The models on multiple solvents take into account both the solute and solvent description and offer the possibility to predict SFEs of any solute in any solvent with root mean squared errors less than 1 kcal/mol. Validations that involve exclusion of fractions or clusters of the solutes or solvents exemplify the model's capability to predict SFEs of novel solutes and solvents with diverse chemical profiles. In addition to being predictive, our models can identify the solute and solvent features that influence SFE predictions. Furthermore, using 3D-RISM hydration thermodynamic output to predict SFEs in any organic solvent reduces the need to run 3D-RISM simulations in all these solvents. Altogether, our multisolvent models for SFE predictions that take advantage of the solvation effects are expected to have an impact in the property prediction space.
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Affiliation(s)
- Vigneshwari Subramanian
- Drug Metabolism and Pharmacokinetics, Research and Early Development-Respiratory, Inflammation and Autoimmune, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, SE-431 83, Mölndal, Sweden.,Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - Ekaterina Ratkova
- Medicinal Chemistry, Research and Early Development - Cardiovascular, Renal and Metabolism, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - David Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - Ola Engkvist
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - Maxim Fedorov
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Moscow, 143026, Russia.,Department of Physics, Scottish Universities Physics Alliance (SUPA), University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, U.K
| | - Antonio Llinas
- Drug Metabolism and Pharmacokinetics, Research and Early Development-Respiratory, Inflammation and Autoimmune, Biopharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
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5
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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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An assessment of the sigma enlarging bridge function for a Lennard-Jones solution using a solvent-solvent correlation function obtained from molecular dynamics simulation. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Tanimoto S, Yoshida N, Yamaguchi T, Ten-no SL, Nakano H. Effect of Molecular Orientational Correlations on Solvation Free Energy Computed by Reference Interaction Site Model Theory. J Chem Inf Model 2019; 59:3770-3781. [DOI: 10.1021/acs.jcim.9b00330] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shoichi Tanimoto
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Norio Yoshida
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tsuyoshi Yamaguchi
- Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan
| | - Seiichiro L. Ten-no
- Graduate School of Science, Technology, and Innovation, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Haruyuki Nakano
- Department of Chemistry, Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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9
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Kido K. A noniterative mean‐field QM/MM‐type approach with a linear response approximation toward an efficient free‐energy evaluation. J Comput Chem 2019; 40:2072-2085. [DOI: 10.1002/jcc.25844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/22/2019] [Accepted: 04/01/2019] [Indexed: 01/23/2023]
Affiliation(s)
- Kentaro Kido
- Nuclear Safety Research CenterJapan Atomic Energy Agency 2‐4 Shirane, Shirakata, Tokai‐mura Ibaraki 319‐1195 Naka‐gun Japan
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10
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Sumi T, Maruyama Y, Mitsutake A, Mochizuki K, Koga K. Application of reference‐modified density functional theory: Temperature and pressure dependences of solvation free energy. J Comput Chem 2017; 39:202-217. [DOI: 10.1002/jcc.25101] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/04/2023]
Affiliation(s)
- Tomonari Sumi
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
- Department of Chemistry, Faculty of ScienceOkayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
| | - Yutaka Maruyama
- Co‐Design Team, FLAGSHIP 2020 Project, RIKEN Advanced Institute for Computational Science, 7‐1‐26, Minatojima‐minami‐machiKobe650‐0047 Japan
| | - Ayori Mitsutake
- Department of PhysicsKeio University, 3‐14‐1 Hiyoshi, Kohoku‐kuYokohama Kanagawa223–8522 Japan
| | - Kenji Mochizuki
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
| | - Kenichiro Koga
- Division of Superconducting and Functional MaterialsResearch Institute for Interdisciplinary Science, Okayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
- Department of Chemistry, Faculty of ScienceOkayama University, 3‐1‐1 Tsushima‐Naka, Kita‐kuOkayama700‐8530 Japan
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11
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Fujita T, Yamamoto T. Assessing the accuracy of integral equation theories for nano-sized hydrophobic solutes in water. J Chem Phys 2017; 147:014110. [DOI: 10.1063/1.4990502] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Takeshi Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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12
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Sumi T, Maruyama Y, Mitsutake A, Koga K. A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution. J Chem Phys 2016; 144:224104. [DOI: 10.1063/1.4953191] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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13
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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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14
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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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15
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Sumi T, Mitsutake A, Maruyama Y. A solvation-free-energy functional: A reference-modified density functional formulation. J Comput Chem 2015; 36:1359-69. [DOI: 10.1002/jcc.23942] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/26/2015] [Accepted: 03/29/2015] [Indexed: 01/21/2023]
Affiliation(s)
- Tomonari Sumi
- Department of Chemistry; Faculty of Science, Okayama University; 3-1-1 Tsushima-Naka Kita-ku Okayama 700-8530 Japan
| | - Ayori Mitsutake
- Department of Physics; Keio University; 3-14-1, Hiyoshi Kohoku-ku, Yokohama Kanagawa 223-8522 Japan
- JST, PREST; 3-14-1 Hiyoshi Kohoku-ku, Yokohama Kanagawa 223-8522 Japan
| | - Yutaka Maruyama
- Department of Physics; Keio University; 3-14-1, Hiyoshi Kohoku-ku, Yokohama Kanagawa 223-8522 Japan
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16
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Miyata T, Thapa J. Accuracy of solvation free energy calculated by hypernetted chain and Kovalenko–Hirata approximations for two-component system of Lennard-Jones liquid. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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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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Truchon JF, Pettitt BM, Labute P. A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies. J Chem Theory Comput 2014; 10:934-941. [PMID: 24634616 PMCID: PMC3953892 DOI: 10.1021/ct4009359] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 01/25/2023]
Abstract
![]()
We show that an Ng
bridge function modified version of the three-dimensional
reference interaction site model (3D-RISM-NgB) solvation free energy
method can accurately predict the hydration free energy (HFE) of a
set of 504 organic molecules. To achieve this, a single unique constant
parameter was adjusted to the computed HFE of single atom Lennard-Jones
solutes. It is shown that 3D-RISM is relatively accurate at predicting
the electrostatic component of the HFE without correction but requires
a modification of the nonpolar contribution that originates in the
formation of the cavity created by the solute in water. We use a free
energy functional with the Ng scaling of the direct correlation function
[Ng, K. C. J. Chem. Phys.1974, 61, 2680]. This produces a rapid, reliable small molecule
HFE calculation for applications in drug design.
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Affiliation(s)
- Jean-François Truchon
- Chemical Computing Group Inc. , 1010 Sherbrooke Street West, Suite 910, Montréal, Québec, Canada , H3A 2R7
| | - B Montgomery Pettitt
- Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas 77555, United States of America
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street West, Suite 910, Montréal, Québec, Canada , H3A 2R7
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Sato H. A modern solvation theory: quantum chemistry and statistical chemistry. Phys Chem Chem Phys 2013; 15:7450-65. [DOI: 10.1039/c3cp50247c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fedotova MV, Kruchinin SE. Hydration of methylamine and methylammonium ion: structural and thermodynamic properties from the data of the integral equation method in the RISM approximation. Russ Chem Bull 2012. [DOI: 10.1007/s11172-012-0034-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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21
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Ratkova EL. A semiempirical model for estimating the hydration free energy of neutral nonpolar compounds. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412100196] [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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22
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Ratkova EL. A comparative analysis of models for hydration free energy calculations using the RISM theory of integral equations. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412060222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Fedotova MV, Kruchinin SE. Hydration of acetic acid and acetate ion in water studied by 1D-RISM theory. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2011.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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25
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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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Palmer DS, Frolov AI, Ratkova EL, Fedorov MV. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:492101. [PMID: 21406779 DOI: 10.1088/0953-8984/22/49/492101] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).
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Affiliation(s)
- David S Palmer
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
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27
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Ratkova EL, Chuev GN, Sergiievskyi VP, Fedorov MV. An Accurate Prediction of Hydration Free Energies by Combination of Molecular Integral Equations Theory with Structural Descriptors. J Phys Chem B 2010; 114:12068-79. [DOI: 10.1021/jp103955r] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ekaterina L. Ratkova
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Gennady N. Chuev
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Volodymyr P. Sergiievskyi
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
| | - Maxim V. Fedorov
- The Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany, and Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region, 142290, Russia
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28
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Palmer DS, Sergiievskyi VP, Jensen F, Fedorov MV. Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model. J Chem Phys 2010; 133:044104. [DOI: 10.1063/1.3458798] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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29
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Yamazaki T, Kovalenko A, Murashov VV, Patey GN. Ion solvation in a water-urea mixture. J Phys Chem B 2010; 114:613-9. [PMID: 19947642 DOI: 10.1021/jp908814t] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We employ molecular dynamics simulations and the reference interaction site model (RISM) integral equation theory to study the solvation structure and solvation thermodynamics of the transfer process from water to a water-urea mixture. Simple positive and negative ions together with uncharged species of the same size are used as crude models for the hydrophilic and hydrophobic groups of a protein. We find that urea preferentially solvates positively charged species. The solvation free energies obtained indicate that larger solutes favor the transfer from water to a water-urea mixture. The decomposition of the transfer free energy into the energetic and entropic terms shows that the energetic part is much larger than the entropic one and tends to dominate the transfer process, supporting the direct mechanism of urea-denaturation. In addition, the effect of urea on the water liquid structure is discussed from the viewpoint of solvation entropy.
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Affiliation(s)
- Takeshi Yamazaki
- National Institute for Nanotechnology, 11421 Saskatchewan Drive, Edmonton, Alberta, T6G 2M9, Canada
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30
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Ten-no S, Jung J, Chuman H, Kawashima Y. Assessment of free energy expressions in RISM integral equation theory: theoretical prediction of partition coefficients revisited. Mol Phys 2010. [DOI: 10.1080/00268970903451848] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Chuev GN, Fedorov MV. Reference interaction site model study of self-aggregating cyanine dyes. J Chem Phys 2009; 131:074503. [DOI: 10.1063/1.3211948] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Sobolev EV, Sobolev OV, Tikhonov DA. Online resource for theoretical study of hydration of biopolymers. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2008; 19:303-315. [PMID: 18484500 DOI: 10.1080/10629360802083707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An online resource has been developed for the theoretical study of hydration of biopolymers by the RISM (Reference Interaction Site Model) method, deriving from the integral equation theory of liquids. The online resource is based upon original software developed by the authors and includes all steps in studying a biopolymer with a given spatial structure and force field. It prepares the input data and carries out the RISM calculation yielding the atom-atom correlation functions of the biopolymer with water as solvent. From these functions the algorithm finds atomic partial contributions to the hydration free energy using various free energy expressions from integral equation theory. The calculated results are automatically recorded in a database, and become available on the website as tables of partial thermodynamic quantities. In addition, the website displays an interactive 3D model of a given molecule, the atoms of which can be painted in different colors in accordance with their partial contributions to the thermodynamic quantity chosen by the user. The user can interactively choose atoms on this molecule and their correlation functions will be displayed. The aim of our work was to develop and present a publicly-accessible resource on the basis of original software which could be used for scientific and educational purposes.
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Affiliation(s)
- E V Sobolev
- Institute of Mathematical Problems of Biology RAS, Pushchino, Russia.
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33
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Kloss T, Heil J, Kast SM. Quantum Chemistry in Solution by Combining 3D Integral Equation Theory with a Cluster Embedding Approach. J Phys Chem B 2008; 112:4337-43. [DOI: 10.1021/jp710680m] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Thomas Kloss
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstraβe 20, 64287 Darmstadt, Germany
| | - Jochen Heil
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstraβe 20, 64287 Darmstadt, Germany
| | - Stefan M. Kast
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Petersenstraβe 20, 64287 Darmstadt, Germany
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34
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Freedman H, Le L, Tuszynski JA, Truong TN. Improving the Performance of the Coupled Reference Interaction Site Model−Hyper-netted Chain (RISM−HNC)/Simulation Method for Free Energy of Solvation. J Phys Chem B 2008; 112:2340-8. [DOI: 10.1021/jp077179l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Holly Freedman
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
| | - Ly Le
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
| | - Jack A. Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
| | - Thanh N. Truong
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
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35
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Chuman H. Toward basic understanding of the partition coefficient log P and its application in QSAR. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2008; 19:71-79. [PMID: 18311635 DOI: 10.1080/10629360701844050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The log P value has been the first choice for the molecular hydrophobicity descriptor in QSAR studies. However, it is still now difficult to understand the partitioning phenomenon in terms of physical chemistry. First, an attempt to understand and predict log P is addressed. We formulated a simple model that expressed by the solvent accessible surface area and the solvation energy difference between aqueous and solvent phases. Next, an application of log P in QSAR analyses of ligand-CYP (Cytochrome P450) interaction was described. Azole compounds are widely used as antifungal agents. We showed that the binding affinity of 18 azole compounds with CYP2B and CYP3A were nicely expressed by the bilinear model of log P. These results suggest that molecular hydrophobicity plays a major role in the binding affinity. The binding mechanism was discussed based on the correlation equations.
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Affiliation(s)
- H Chuman
- Institute of Health Biosciences, University of Tokushima, Graduate School, Tokushima, Japan.
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36
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Costa D, Munaó G, Saija F, Caccarno C. Reference interaction site model and molecular dynamics study of structure and thermodynamics of methanol. J Chem Phys 2007; 127:224501. [DOI: 10.1063/1.2803059] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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37
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Chuev GN, Fedorov MV, Crain J. Improved estimates for hydration free energy obtained by the reference interaction site model. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.10.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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