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Imamura K, Yokogawa D, Sato H. Recent developments and applications of reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED): A hybrid model of quantum chemistry and integral equation theory of molecular liquids. J Chem Phys 2024; 160:050901. [PMID: 38341702 DOI: 10.1063/5.0190116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/13/2024] Open
Abstract
The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications.
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Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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2
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Jang T, Paik D, Shin S, Kim H. Density functional theory in classical explicit solvents: Mean‐field
QM
/
MM
method for simulating solid–liquid interfaces. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Taehwan Jang
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Dooam Paik
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Seung‐Jae Shin
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
| | - Hyungjun Kim
- Department of Chemistry Korea Advanced Institute of Science and Technology (KAIST) Daejeon Republic of Korea
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3
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Reimann M, Kaupp M. Evaluation of an Efficient 3D-RISM-SCF Implementation as a Tool for Computational Spectroscopy in Solution. J Phys Chem A 2020; 124:7439-7452. [PMID: 32838530 DOI: 10.1021/acs.jpca.0c06322] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The 3D-RISM-SCF solvent-model implementation of Gusarov et al. [ J. Phys. Chem. A 2006, 110, 6083-6090] in the Amsterdam density functional program has been improved and extended. In particular, an accurate yet efficient representation of the solute electrostatic potential is provided. The Coulomb-potential fitting of many DFT codes can be used advantageously in this context. The extra effort compared to a point-charge representation is small for a given SCF cycle and compensated by faster SCF convergence. This allows applications to large solutes, as demonstrated by evaluation of the solvatochromism of Reichardt's dye. In general, TDDFT applications to excitation energies in solution stand out and are highlighted. Applications to the 17O NMR chemical shifts of N-methylformamide in different solvents also demonstrate the distinct advantages of 3D-RISM over continuum solvents. Limitations are observed in this case for water solvent, where the solvent shielding is overestimated. This shortcoming applies also to the 17O gas-to-liquid shift of water, where we used localized molecular orbital analyses for a deeper understanding. For such cases of extremely strong solute-solvent interactions, couplings between solute and solvent orbitals induced by the magnetic perturbation are relevant. These clearly require a quantum-mechanical treatment of the most closely bound solvent molecules. Except for such extreme cases, 3D-RISM-SCF is very well suited to treat solvent effects on NMR parameters. More serious limitations pertain to the treatment of vibrational spectra, where the absence of the coupling between solute and solvent vibrational modes limits the accuracy of applications of 3D-RISM-SCF. The reported extended, efficient, and numerically accurate 3D-RISM-SCF implementation should provide a useful tool to study chemical and spectroscopic properties of molecules of appreciable size in a realistic solvent environment.
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Affiliation(s)
- Marc Reimann
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, D-10623, Berlin, Germany
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4
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Gauthier JA, Dickens CF, Heenen HH, Vijay S, Ringe S, Chan K. Unified Approach to Implicit and Explicit Solvent Simulations of Electrochemical Reaction Energetics. J Chem Theory Comput 2019; 15:6895-6906. [DOI: 10.1021/acs.jctc.9b00717] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph A. Gauthier
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Colin F. Dickens
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Hendrik H. Heenen
- Department of Physics, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Sudarshan Vijay
- Department of Physics, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
| | - Stefan Ringe
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Karen Chan
- Department of Physics, Technical University of Denmark, DK-2800, Kongens Lyngby, Denmark
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5
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Gauthier JA, Dickens CF, Ringe S, Chan K. Practical Considerations for Continuum Models Applied to Surface Electrochemistry. Chemphyschem 2019; 20:3074-3080. [PMID: 31317628 DOI: 10.1002/cphc.201900536] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/17/2019] [Indexed: 11/11/2022]
Abstract
Modelling the electrolyte at the electrochemical interface remains a major challenge in ab initio simulations of charge transfer processes at surfaces. Recently, the development of hybrid polarizable continuum models/ab initio models have allowed for the treatment of solvation and electrolyte charge in a computationally efficient way. However, challenges remain in its application. Recent literature has reported that large cell heights are required to reach convergence, which presents a serious computational cost. Furthermore, calculations of reaction energetics require costly iterations to tune the surface charge to the desired potential. In this work, we present a simple capacitor model of the interface that illuminates how to circumvent both of these challenges. We derive a correction to the energy for finite cell heights to obtain the large cell energies at no additional computational expense. We furthermore demonstrate that the reaction energetics determined at constant charge are easily mapped to those at constant potential, which eliminates the need to apply iterative schemes to tune the system to a constant potential. These developments together represent more than an order of magnitude reduction of the computational overhead required for the application of polarizable continuum models to surface electrochemistry.
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Affiliation(s)
- Joseph A Gauthier
- SUNCAT Center for Interface Science and Catalysis Department of Chemical Engineering, Stanford University, Stanford, California, 94305, United States
| | - Colin F Dickens
- SUNCAT Center for Interface Science and Catalysis Department of Chemical Engineering, Stanford University, Stanford, California, 94305, United States
| | - Stefan Ringe
- SUNCAT Center for Interface Science and Catalysis Department of Chemical Engineering, Stanford University, Stanford, California, 94305, United States
| | - Karen Chan
- Department of Physics Technical University of Denmark DK-2800, Kgs. Lyngby, Denmark
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6
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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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7
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Gauthier JA, Ringe S, Dickens CF, Garza AJ, Bell AT, Head-Gordon M, Nørskov JK, Chan K. Challenges in Modeling Electrochemical Reaction Energetics with Polarizable Continuum Models. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02793] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph A. Gauthier
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Stefan Ringe
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Colin F. Dickens
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Alejandro J. Garza
- The Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
| | - Alexis T. Bell
- The Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- The Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley California 94720, United States
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jens K. Nørskov
- SUNCAT Center for Interface Science and Catalysis, Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Karen Chan
- SUNCAT Center for Interface Science and Catalysis, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, United States
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8
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Kido K, Kasahara K, Yokogawa D, Sato H. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach. J Chem Phys 2015; 143:014103. [PMID: 26156461 DOI: 10.1063/1.4923007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
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Affiliation(s)
- Kentaro Kido
- Nuclear Safety Research Center, Japan Atomic Energy Agency, 2-4 Shirane, Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Kento Kasahara
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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9
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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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10
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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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11
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Nishiyama K, Watanabe Y, Yoshida N, Hirata F. Solvent dependence of Stokes shift for organic solute–solvent systems: A comparative study by spectroscopy and reference interaction-site model–self-consistent-field theory. J Chem Phys 2013; 139:094503. [DOI: 10.1063/1.4819268] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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12
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Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials. PURE APPL CHEM 2013. [DOI: 10.1351/pac-con-12-06-03] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Statistical–mechanical, 3D-RISM-KH molecular theory of solvation (3D reference interaction site model with the Kovalenko–Hirata closure) is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. 3D-RISM-KH explains the molecular mechanisms of self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), aggregation of prion proteins and β-sheet amyloid oligomers, protein-ligand binding, and function-related solvation properties of complexes as large as the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) and GroEL/ES chaperone. Molecular mechanics/Poisson–Boltzmann (generalized Born) surface area [MM/PB(GB)SA] post-processing of molecular dynamics (MD) trajectories involving SA empirical nonpolar terms is replaced with MM/3D-RISM-KH statistical–mechanical evaluation of the solvation thermodynamics. 3D-RISM-KH has been coupled with multiple time-step (MTS) MD of the solute biomolecule driven by effective solvation forces, which are obtained analytically by converging the 3D-RISM-KH integral equations at outer time-steps and are calculated in between by using solvation force coordinate extrapolation (SFCE) in the subspace of previous solutions to 3D-RISM-KH. The procedure is stabilized by the optimized isokinetic Nosé–Hoover (OIN) chain thermostatting, which enables gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties. The multiscale OIN/SFCE/3D-RISM-KH algorithm is implemented in the Amber package and illustrated on a fully flexible model of alanine dipeptide in aqueous solution, exhibiting the computational rate of solvent sampling 20 times faster than standard MD with explicit solvent. Further substantial acceleration can be achieved with 3D-RISM-KH efficiently sampling essential events with rare statistics such as exchange and localization of solvent, ions, and ligands at binding sites and pockets of the biomolecule. 3D-RISM-KH was coupled with ab initio complete active space self-consistent field (CASSCF) and orbital-free embedding (OFE) Kohn–Sham (KS) density functional theory (DFT) quantum chemistry methods in an SCF description of electronic structure, optimized geometry, and chemical reactions in solution. The (OFE)KS-DFT/3D-RISM-KH multi-scale method is implemented in the Amsterdam Density Functional (ADF) package and extensively validated against experiment for solvation thermochemistry, photochemistry, conformational equilibria, and activation barriers of various nanosystems in solvents and ionic liquids (ILs). Finally, the replica RISM-KH-VM molecular theory for the solvation structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous materials reveals the molecular mechanisms of sorption and supercapacitance in nanoporous carbon electrodes, which is drastically different from a planar electrical double layer.
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13
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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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14
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Omelyan I, Kovalenko A. Generalised canonical–isokinetic ensemble: speeding up multiscale molecular dynamics and coupling with 3D molecular theory of solvation. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.700486] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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15
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Gusarov S, Pujari BS, Kovalenko A. Efficient treatment of solvation shells in 3D molecular theory of solvation. J Comput Chem 2012; 33:1478-94. [DOI: 10.1002/jcc.22974] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 03/02/2012] [Indexed: 01/01/2023]
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16
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Helgaker T, Coriani S, Jørgensen P, Kristensen K, Olsen J, Ruud K. Recent Advances in Wave Function-Based Methods of Molecular-Property Calculations. Chem Rev 2012; 112:543-631. [DOI: 10.1021/cr2002239] [Citation(s) in RCA: 463] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Trygve Helgaker
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via Giorgieri 1, I-34127 Trieste, Italy
| | - Poul Jørgensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Jeppe Olsen
- Lundbeck Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Kenneth Ruud
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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17
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Kiyota Y, Yoshida N, Hirata F. A New Approach for Investigating the Molecular Recognition of Protein: Toward Structure-Based Drug Design Based on the 3D-RISM Theory. J Chem Theory Comput 2011; 7:3803-15. [PMID: 26598271 DOI: 10.1021/ct200358h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A new approach to investigate a molecular recognition process of protein is presented based on the three-dimensional reference interaction site model (3D-RISM) theory, a statistical mechanics theory of molecular liquids. Numerical procedure for solving the conventional 3D-RISM equation consists of two steps. In step 1, we solve ordinary RISM (or 1D-RISM) equations for a solvent mixture including target ligands in order to obtain the density pair correlation functions (PCF) among molecules in the solution. Then, we solve the 3D-RISM equation for a solute-solvent system to find three-dimensional density distribution functions (3D-DDF) of solvent species around a protein, using PCF obtained in the first step. A key to the success of the method was to regard a target ligand as one of "solvent" species. However, the success is limited due to a difficulty of solving the 1D-RISM equation for a solvent mixture, including large ligand molecules. In the present paper, we propose a method which eases the limitation concerning solute size in the conventional method. In this approach, we solve a solute-solute 3D-RISM equations for a protein-ligand system in which both proteins and ligands are regarded as "solutes" at infinite dilution. The 3D- and 1D-RISM equations are solved for protein-solvent and ligand-solvent systems, respectively, in order to obtain the 3D- and 1D-DDF of solvent around the solutes, which are required for solving the solute-solute 3D-RISM equation. The method is applied to two practical and noteworthy examples concerning pharmaceutical design. One is an odorant binding protein in the Drosophila melanogaster , which binds an ethanol molecule. The other is phospholipase A2, which is known as a receptor of acetylsalicylic acid or aspirin. The result indicates that the method successfully reproduces the binding mode of the ligand molecules in the binding sites measured by the experiments.
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Affiliation(s)
- Yasuomi Kiyota
- Department of Theoretical Molecular Science, Institute for Molecular Science , Okazaki 444-8585, Japan
| | - Norio Yoshida
- Department of Theoretical Molecular Science, Institute for Molecular Science , Okazaki 444-8585, Japan.,Department of Functional Molecular Science, The Graduate University for Advanced Studies , Okazaki 444-8585, Japan
| | - Fumio Hirata
- Department of Theoretical Molecular Science, Institute for Molecular Science , Okazaki 444-8585, Japan.,Department of Functional Molecular Science, The Graduate University for Advanced Studies , Okazaki 444-8585, Japan
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18
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Yoshida N, Kiyota Y, Hirata F. The electronic-structure theory of a large-molecular system in solution: Application to the intercalation of proflavine with solvated DNA. J Mol Liq 2011. [DOI: 10.1016/j.molliq.2010.04.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Marenich AV, Cramer CJ, Truhlar DG. Sorting Out the Relative Contributions of Electrostatic Polarization, Dispersion, and Hydrogen Bonding to Solvatochromic Shifts on Vertical Electronic Excitation Energies. J Chem Theory Comput 2010; 6:2829-44. [DOI: 10.1021/ct100267s] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Aleksandr V. Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J. Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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20
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Mennucci B, da Silva CO. A Quantum Mechanical Strategy to Investigate the Structure of Liquids: The Cases of Acetonitrile, Formamide, and Their Mixture. J Phys Chem B 2008; 112:6803-13. [DOI: 10.1021/jp8009657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, Pisa, Italy, Departamento de Química, Universidade Federal Rural Rio de Janeiro, BR465 km 47, Rio de Janeiro 23890-000, Brazil
| | - Clarissa O. da Silva
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, via Risorgimento 35, Pisa, Italy, Departamento de Química, Universidade Federal Rural Rio de Janeiro, BR465 km 47, Rio de Janeiro 23890-000, Brazil
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21
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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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Lin, Gao J. Solvatochromic Shifts of the n → π* Transition of Acetone from Steam Vapor to Ambient Aqueous Solution: A Combined Configuration Interaction QM/MM Simulation Study Incorporating Solvent Polarization. J Chem Theory Comput 2007; 3:1484-93. [DOI: 10.1021/ct700058c] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Lin
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, Digital Technology Center, University of Minnesota, 207 Pleasant Street, SE, Minneapolis, Minnesota 55455
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