1
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Ishizuka R. Martini 3D-OZ: A Theoretical Investigation of Solvation Shell Structures and Solvation Free Energies of Martini Coarse-Grained Proteins. J Phys Chem B 2024; 128:8522-8529. [PMID: 39180742 DOI: 10.1021/acs.jpcb.4c03897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
Abstract
We investigate the properties of aqueous solutions using integral equation theories and molecular dynamics (MD) simulations within the framework of the MARTINI coarse-grained force field. The integral equation theory used in the present work is based on the Ornstein-Zernike equation coupled with the hypernetted chain (HNC) and Kovalenko-Hirata (KH) closures. Overall, the solvation shell structures and solvation thermodynamics in the HNC approximation are shown to be in better agreement with those from the MD simulation than the KH results. Especially, through the analysis of spatial distribution functions of water around a protein, we have demonstrated that the HNC approximation can provide the highly anisotropic structure of the solvation shell of the protein. On the other hand, the KH approximation works well for simple particle solutes, but the results for highly hydrated proteins deviate quite significantly from the MD results. We further explore in detail the reason underlying the deviation caused by the KH approximation. Lastly, a potential application of the integral equation theory with the MARTINI model is outlined.
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Affiliation(s)
- Ryosuke Ishizuka
- Zkanics F.P.S., Side-6 Senriyama-West, Suita, Osaka 565-0851, Japan
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2
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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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3
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Gray JG, Giambaşu GM, Case DA, Luchko T. Integral equation models for solvent in macromolecular crystals. J Chem Phys 2022; 156:014801. [PMID: 34998331 PMCID: PMC8889494 DOI: 10.1063/5.0070869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The solvent can occupy up to ∼70% of macromolecular crystals, and hence, having models that predict solvent distributions in periodic systems could improve the interpretation of crystallographic data. Yet, there are few implicit solvent models applicable to periodic solutes, and crystallographic structures are commonly solved assuming a flat solvent model. Here, we present a newly developed periodic version of the 3D-reference interaction site model (RISM) integral equation method that is able to solve efficiently and describe accurately water and ion distributions in periodic systems; the code can compute accurate gradients that can be used in minimizations or molecular dynamics simulations. The new method includes an extension of the Ornstein–Zernike equation needed to yield charge neutrality for charged solutes, which requires an additional contribution to the excess chemical potential that has not been previously identified; this is an important consideration for nucleic acids or any other charged system where most or all the counter- and co-ions are part of the “disordered” solvent. We present several calculations of proteins, RNAs, and small molecule crystals to show that x-ray scattering intensities and the solvent structure predicted by the periodic 3D-RISM solvent model are in closer agreement with the experiment than are intensities computed using the default flat solvent model in the refmac5 or phenix refinement programs, with the greatest improvement in the 2 to 4 Å range. Prospects for incorporating integral equation models into crystallographic refinement are discussed.
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Affiliation(s)
- Jonathon G Gray
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - George M Giambaşu
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Tyler Luchko
- Department of Physics and Astronomy, California State University, Northridge, California 91330, USA
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4
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Nie C, Geng J, Marlow WH. Formation free energy of an i-mer at spinodal. J Chem Phys 2021; 154:234108. [PMID: 34241258 DOI: 10.1063/5.0051879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In statistical mechanics, the formation free energy of an i-mer can be understood as the Gibbs free energy change in a system consisting of pure monomers after and prior to the formation of the i-mer. For molecules interacting via Lennard-Jones potential, we have computed the formation free energy of a Stillinger i-mer [F. H. Stillinger, J. Chem. Phys. 38, 1486 (1963)] and a ten Wolde-Frenkel (tWF) [P. R. ten Wolde and D. Frenkel, J. Chem. Phys. 109, 9901 (1998)] i-mer at spinodal at reduced temperatures from 0.7 to 1.2. It turns out that the size of a critical Stillinger i-mer remains finite and its formation free energy is on the order of kBT, and the size of a critical tWF i-mer remains finite and its formation free energy is even higher. This can be explained by Binder's theory [K. Binder, Phys. Rev. A 29, 341 (1984)] that for a system, when approaching spinodal, if the Ginzburg criterion is not satisfied, a gradual transition will take place from nucleation to spinodal decomposition, where the free-energy barrier height is on the order of kBT.
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Affiliation(s)
- Chu Nie
- School of Power and Mechanical Engineering, Wuhan University, Wuhan 430072, China
| | - Jun Geng
- State Power Investment Cooperation Hydrogen Energy Development Co., Ltd., South Park, Bejing Future Science & Technology Park, Beijing 100029, China
| | - William H Marlow
- Nuclear Engineering Department, Texas A&M University, 3133 TAMU, College Station, Texas 77843-3133, USA
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5
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Akiyama R, Annaka M, Kohda D, Kubota H, Maeda Y, Matsumori N, Mizuno D, Yoshida N. Biophysics at Kyushu University. Biophys Rev 2020; 12:245-247. [PMID: 32067193 PMCID: PMC7242550 DOI: 10.1007/s12551-020-00643-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/09/2020] [Indexed: 12/13/2022] Open
Affiliation(s)
- Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka, 819-0395, Japan.
| | - Masahiko Annaka
- Department of Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
| | - Daisuke Kohda
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hiroyuki Kubota
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yusuke Maeda
- Department of Physics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Nobuaki Matsumori
- Department of Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
| | - Daisuke Mizuno
- Department of Physics, Kyushu University, Fukuoka, 819-0395, Japan
| | - Norio Yoshida
- Department of Chemistry, Kyushu University, Fukuoka, 819-0395, Japan
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6
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Accurate and rapid calculation of hydration free energy and its physical implication for biomolecular functions. Biophys Rev 2020; 12:469-480. [PMID: 32180122 DOI: 10.1007/s12551-020-00686-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2020] [Indexed: 01/19/2023] Open
Abstract
Here we review a new method for calculating a hydration free energy (HFE) of a solute and discuss its physical implication for biomolecular functions in aqueous environments. The solute hydration is decomposed into processes 1 and 2. A cavity matching the geometric characteristics of the solute at the atomic level is created in process 1. Solute-water van der Waals and electrostatic interaction potentials are incorporated in process 2. The angle-dependent integral equation theory combined with our morphometric approach is applied to process 1, and the three-dimensional reference interaction site model theory is employed for process 2. Molecular models are adopted for water. The new method is characterized by the following. Solutes with various sizes including proteins can be treated in the same manner. It is almost as accurate as the molecular dynamics simulation despite its far smaller computational burden. It enables us to handle a solute possessing a significantly large total charge without difficulty. The HFE can be decomposed into a variety of physically insightful, energetic, and entropic components. It is best suited to the elucidation of mechanisms of protein folding, pressure and cold denaturation of a protein, and different types of molecular recognition.
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7
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Vyalov I, Rocchia W. Including diverging electrostatic potential in 3D-RISM theory: The charged wall case. J Chem Phys 2018; 148:114106. [PMID: 29566525 DOI: 10.1063/1.5019596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Although three-dimensional site-site molecular integral equations of liquids are a powerful tool of the modern theoretical chemistry, their applications to the problem of characterizing the electrical double layer originating at the solid-liquid interface with a macroscopic substrate are severely limited by the fact that an infinitely extended charged plane generates a divergent electrostatic potential. Such potentials cannot be treated within the standard 3D-Reference Interaction Site Model equation solution framework since it leads to functions that are not Fourier transformable. In this paper, we apply a renormalization procedure to overcome this obstacle. We then check the validity and numerical accuracy of the proposed computational scheme on the prototypical gold (111) surface in contact with water/alkali chloride solution. We observe that despite the proposed method requires, to achieve converged charge densities, a higher spatial resolution than that suited to the estimation of biomolecular solvation with either 3D-RISM or continuum electrostatics approaches, it still is computationally efficient. Introducing the electrostatic potential of an infinite wall, which is periodic in 2 dimensions, we avoid edge effects, permit a robust integration of Poisson's equation, and obtain the 3D electrostatic potential profile for the first time in such calculations. We show that the potential within the electrical double layer presents oscillations which are not grasped by the Debye-Hückel and Gouy-Chapman theories. This electrostatic potential deviates from its average of up to 1-2 V at small distances from the substrate along the lateral directions. Applications of this theoretical development are relevant, for example, for liquid scanning tunneling microscopy imaging.
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Affiliation(s)
- Ivan Vyalov
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Walter Rocchia
- CONCEPT Lab, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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8
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Cao S, Zhu L, Huang X. 3DRISM-HI-D2MSA: an improved analytic theory to compute solvent structure around hydrophobic solutes with proper treatment of solute–solvent electrostatic interactions. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1416195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Siqin Cao
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Lizhe Zhu
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Xuhui Huang
- Department of Chemistry, Center of Systems Biology and Human Health, State Key Laboratory of Molecular Neuroscience, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, The Hong Kong University of Science and Technology, Kowloon, Hong Kong
- HKUST-Shenzhen Research Institute, Hi-Tech Park, Nanshan, Shenzhen, China
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9
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Yoshida N. Role of Solvation in Drug Design as Revealed by the Statistical Mechanics Integral Equation Theory of Liquids. J Chem Inf Model 2017; 57:2646-2656. [DOI: 10.1021/acs.jcim.7b00389] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norio Yoshida
- Department of Chemistry,
Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 Japan
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10
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Okumura H, Higashi M, Yoshida Y, Sato H, Akiyama R. Theoretical approaches for dynamical ordering of biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:212-228. [PMID: 28988931 DOI: 10.1016/j.bbagen.2017.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 01/21/2023]
Abstract
BACKGROUND Living systems are characterized by the dynamic assembly and disassembly of biomolecules. The dynamical ordering mechanism of these biomolecules has been investigated both experimentally and theoretically. The main theoretical approaches include quantum mechanical (QM) calculation, all-atom (AA) modeling, and coarse-grained (CG) modeling. The selected approach depends on the size of the target system (which differs among electrons, atoms, molecules, and molecular assemblies). These hierarchal approaches can be combined with molecular dynamics (MD) simulation and/or integral equation theories for liquids, which cover all size hierarchies. SCOPE OF REVIEW We review the framework of quantum mechanical/molecular mechanical (QM/MM) calculations, AA MD simulations, CG modeling, and integral equation theories. Applications of these methods to the dynamical ordering of biomolecular systems are also exemplified. MAJOR CONCLUSIONS The QM/MM calculation enables the study of chemical reactions. The AA MD simulation, which omits the QM calculation, can follow longer time-scale phenomena. By reducing the number of degrees of freedom and the computational cost, CG modeling can follow much longer time-scale phenomena than AA modeling. Integral equation theories for liquids elucidate the liquid structure, for example, whether the liquid follows a radial distribution function. GENERAL SIGNIFICANCE These theoretical approaches can analyze the dynamic behaviors of biomolecular systems. They also provide useful tools for exploring the dynamic ordering systems of biomolecules, such as self-assembly. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Hisashi Okumura
- Research Center for Computational Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Structural Molecular Science, The Graduate University for Advanced Studies, Okazaki, Aichi 444-8585, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan
| | - Yuichiro Yoshida
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Japan
| | - Ryo Akiyama
- Department of Chemistry, Kyushu University, Fukuoka 819-0395, Japan
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11
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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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12
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Hayashi T, Oshima H, Harano Y, Kinoshita M. Water based on a molecular model behaves like a hard-sphere solvent for a nonpolar solute when the reference interaction site model and related theories are employed. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:344003. [PMID: 27366886 DOI: 10.1088/0953-8984/28/34/344003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
For neutral hard-sphere solutes, we compare the reduced density profile of water around a solute g(r), solvation free energy μ, energy U, and entropy S under the isochoric condition predicted by the two theories: dielectrically consistent reference interaction site model (DRISM) and angle-dependent integral equation (ADIE) theories. A molecular model for water pertinent to each theory is adopted. The hypernetted-chain (HNC) closure is employed in the ADIE theory, and the HNC and Kovalenko-Hirata (K-H) closures are tested in the DRISM theory. We also calculate g(r), U, S, and μ of the same solute in a hard-sphere solvent whose molecular diameter and number density are set at those of water, in which case the radial-symmetric integral equation (RSIE) theory is employed. The dependences of μ, U, and S on the excluded volume and solvent-accessible surface area are analyzed using the morphometric approach (MA). The results from the ADIE theory are in by far better agreement with those from computer simulations available for g(r), U, and μ. For the DRISM theory, g(r) in the vicinity of the solute is quite high and becomes progressively higher as the solute diameter d U increases. By contrast, for the ADIE theory, it is much lower and becomes further lower as d U increases. Due to unphysically positive U and significantly larger |S|, μ from the DRISM theory becomes too high. It is interesting that μ, U, and S from the K-H closure are worse than those from the HNC closure. Overall, the results from the DRISM theory with a molecular model for water are quite similar to those from the RSIE theory with the hard-sphere solvent. Based on the results of the MA analysis, we comparatively discuss the different theoretical methods for cases where they are applied to studies on the solvation of a protein.
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Affiliation(s)
- Tomohiko Hayashi
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
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13
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Johnson J, Case DA, Yamazaki T, Gusarov S, Kovalenko A, Luchko T. Small molecule hydration energy and entropy from 3D-RISM. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:344002. [PMID: 27367817 PMCID: PMC5118872 DOI: 10.1088/0953-8984/28/34/344002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Implicit solvent models offer an attractive way to estimate the effects of a solvent environment on the properties of small or large solutes without the complications of explicit simulations. One common test of accuracy is to compute the free energy of transfer from gas to liquid for a variety of small molecules, since many of these values have been measured. Studies of the temperature dependence of these values (i.e. solvation enthalpies and entropies) can provide additional insights into the performance of implicit solvent models. Here, we show how to compute temperature derivatives of hydration free energies for the 3D-RISM integral equation approach. We have computed hydration free energies of 1123 small drug-like molecules (both neutral and charged). Temperature derivatives were also used to calculate hydration energies and entropies of 74 of these molecules (both neutral and charged) for which experimental data is available. While direct results have rather poor agreement with experiment, we have found that several previously proposed linear hydration free energy correction schemes give good agreement with experiment. These corrections also provide good agreement for hydration energies and entropies though simple extensions are required in some cases.
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Affiliation(s)
- J Johnson
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - D A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854
| | - T Yamazaki
- Vancouver Prostate Centre, 2660 Oak Street, Vancouver, BC, V6H 3Z6, Canada
| | - S Gusarov
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Dr., Edmonton, AB, T6G 2M9, Canada
| | - A Kovalenko
- National Institute for Nanotechnology, National Research Council of Canada, 11421 Saskatchewan Dr., Edmonton, AB, T6G 2M9, Canada
- Department of Mechanical Engineering, University of Alberta, 10-203 Donadeo Innovation Centre for Engineering, 9211-116 Str., Edmonton, AB, T6G 1H9, Canada
| | - T Luchko
- Department of Physics and Astronomy, California State University, Northridge, CA 91330
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14
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Oshima H, Kinoshita M. A highly efficient hybrid method for calculating the hydration free energy of a protein. J Comput Chem 2015; 37:712-23. [DOI: 10.1002/jcc.24253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hiraku Oshima
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
| | - Masahiro Kinoshita
- Institute of Advanced Energy, Kyoto University; Uji Kyoto 611-0011 Japan
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15
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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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16
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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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17
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Zhou S. Effects of discreteness of surface charges on the effective electrostatic interactions. J Chem Phys 2014; 140:234704. [PMID: 24952557 DOI: 10.1063/1.4881601] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- Shiqi Zhou
- School of Physics and Electronics, Central South University, Changsha, Hunan 410083, China
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18
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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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