1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Raposo DJ. Effect of Conformational Equilibrium on Solvation Properties of 1,2-DCE in Water: A Solvation Thermodynamics and 3D-RISM Study. J Phys Chem B 2023; 127:757-765. [PMID: 36626710 DOI: 10.1021/acs.jpcb.2c07836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The contributions of the enthalpy and entropy of solvation for the study of chemical and biological systems are important in the prediction, interpretation, and manipulation of these processes. The relation between solvation Gibbs energies, enthalpies, and entropies of solvation, and their rigorous relation with the conformational equilibrium, are derived for the first time and applied with a computational method, in accordance with the Solvation Thermodynamics previous results, to 1,2-dichloroethane solvation in water. The rigid conformer calculations in solution were performed by using PC+/3D-RISM approach, with the conformational averaged results for enthalpy and solvation Gibbs energy reproducing the experimental results quite successfully. A qualitative agreement in the entropy of solvation predictions was also observed.
Collapse
Affiliation(s)
- Diego J Raposo
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife, Pernambuco50740-560, Brazil
| |
Collapse
|
3
|
Tanaka S, Yamamoto N, Kasahara K, Ishii Y, Matubayasi N. Crystal Growth of Urea and Its Modulation by Additives as Analyzed by All-Atom MD Simulation and Solution Theory. J Phys Chem B 2022; 126:5274-5290. [DOI: 10.1021/acs.jpcb.2c01764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Senri Tanaka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Naoki Yamamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kento Kasahara
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yoshiki Ishii
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
4
|
Yasoshima N, Ishiyama T, Matubayasi N. Adsorption Energetics of Amino Acid Analogs on Polymer/Water Interfaces Studied by All-Atom Molecular Dynamics Simulation and a Theory of Solutions. J Phys Chem B 2022; 126:4389-4400. [PMID: 35653506 DOI: 10.1021/acs.jpcb.2c01297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Energetics of adsorption was addressed with all-atom molecular dynamics simulation on the interfaces of poly(2-methoxyethyl acrylate) (PMEA), poly(methyl methacrylate) (PMMA), and poly(butyl acrylate) (PBA) with water. A wide variety of adsorbate solutes were examined, and the free energy of adsorption was computed with the method of energy representation. It was found that the adsorption free energy was favorable (negative) for all the combinations of solute and polymer, and among PMEA, PMMA, and PBA, the strongest adsorption was observed on PMMA for the hydrophobic solutes and on PMEA for the hydrophilic ones. According to the decomposition of the adsorption free energy into the contributions from polymer and water, it was seen that the polymer contribution is larger in magnitude with the solute size. The total free energy of adsorption was correlated well with the solvation free energy in bulk water only for hydrophobic solutes. The roles of the intermolecular interaction components such as electrostatic, van der Waals, and excluded-volume were further studied, and the electrostatic component was influential only in determining the polymer dependences of the adsorption propensities of hydrophilic solutes. The extent of adsorption was shown to be ranked by the van der Waals component in the solute-polymer interaction separately over the hydrophilic and hydrophobic solutes, with the excluded-volume effect from water pointed out to also drive the adsorption.
Collapse
Affiliation(s)
- Nobuhiro Yasoshima
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Tatsuya Ishiyama
- Department of Applied Chemistry, Graduate School of Science and Engineering, University of Toyama, Toyama 930-8555, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
5
|
Waibl F, Kraml J, Hoerschinger VJ, Hofer F, Kamenik AS, Fernández-Quintero ML, Liedl KR. Grid inhomogeneous solvation theory for cross-solvation in rigid solvents. J Chem Phys 2022; 156:204101. [PMID: 35649837 DOI: 10.1063/5.0087549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Grid Inhomogeneous Solvation Theory (GIST) has proven useful to calculate localized thermodynamic properties of water around a solute. Numerous studies have leveraged this information to enhance structure-based binding predictions. We have recently extended GIST toward chloroform as a solvent to allow the prediction of passive membrane permeability. Here, we further generalize the GIST algorithm toward all solvents that can be modeled as rigid molecules. This restriction is inherent to the method and is already present in the inhomogeneous solvation theory. Here, we show that our approach can be applied to various solvent molecules by comparing the results of GIST simulations with thermodynamic integration (TI) calculations and experimental results. Additionally, we analyze and compare a matrix consisting of 100 entries of ten different solvent molecules solvated within each other. We find that the GIST results are highly correlated with TI calculations as well as experiments. For some solvents, we find Pearson correlations of up to 0.99 to the true entropy, while others are affected by the first-order approximation more strongly. The enthalpy-entropy splitting provided by GIST allows us to extend a recently published approach, which estimates higher order entropies by a linear scaling of the first-order entropy, to solvents other than water. Furthermore, we investigate the convergence of GIST in different solvents. We conclude that our extension to GIST reliably calculates localized thermodynamic properties for different solvents and thereby significantly extends the applicability of this widely used method.
Collapse
Affiliation(s)
- Franz Waibl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Johannes Kraml
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Valentin J Hoerschinger
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Florian Hofer
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Anna S Kamenik
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Department of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innrain 80/82, Innsbruck, Austria
| |
Collapse
|
6
|
Matubayasi N. Solvation energetics of proteins and their aggregates analyzed by all-atom molecular dynamics simulations and the energy-representation theory of solvation. Chem Commun (Camb) 2021; 57:9968-9978. [PMID: 34505117 DOI: 10.1039/d1cc03395f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvation is a controlling factor for the structure and function of proteins. This article addresses the effects of solvation from an energetic perspective for the fluctuations and cosolvent-induced changes in protein structures and the equilibrium of aggregate formation for a peptide. A theoretical framework to analyze the solvation effects with an explicit solvent is introduced by adopting the energy-representation theory of solvation, and the connection of the solvation free energy to the protein structure and the aggregation tendency is quantitatively described in combination with all-atom molecular dynamics simulations. The interaction components that govern the solvation effects on the structural variations of proteins are further identified through correlation analysis, and a computational scheme to assess the shift of an aggregation equilibrium due to the addition of a cosolvent is provided.
Collapse
Affiliation(s)
- Nobuyuki Matubayasi
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan.
| |
Collapse
|
7
|
Kojima H, Handa K, Yamada K, Matubayasi N. Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions. J Phys Chem B 2021; 125:9357-9371. [PMID: 34351173 DOI: 10.1021/acs.jpcb.1c04818] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The performance of a polymer medium as a separation membrane is determined by the dissolution free energy ΔG and diffusion coefficient D of the permeant. In this work, ΔG and D of water are investigated with all-atom molecular dynamics simulation in a wide variety of polymer species in the amorphous state. The computed ΔG is shown to agree well with the experimental value for linear homopolymers, and the degrees of polymerization of the homopolymers do not affect ΔG when they are beyond ∼10. The copolymers of ethylene-vinylidene difluoride, ethylene-vinyl acetate, and ethylene-acrylamide are then examined by changing the repeating patterns of the constituent monomers in both the periodic and graft forms. It is found that ΔG is determined primarily by the overall compositions of the monomers and is not affected by the copolymerization topology (periodic or graft). The hydrophobicity of the copolymer is enhanced, furthermore, when the hydrophobicity and hydrophilicity of the ethylene and non-ethylene parts are well contrasted and those parts are fragmented along the polymer chain. According to the computed D, the diffusivity of water tends to be larger when the (co)polymer is more hydrophobic and ΔG is more positive. D is actually seen to vary by orders of magnitude with the polymer structures, while the effect of the polymer species on the water permeation is stronger for ΔG than for D.
Collapse
Affiliation(s)
- Hidekazu Kojima
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kazuya Handa
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kazuo Yamada
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
8
|
Chuev GN, Fedotova MV, Valiev M. Renormalized site density functional theory for models of ion hydration. J Chem Phys 2021; 155:064501. [PMID: 34391371 DOI: 10.1063/5.0060249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The development of accurate statistical mechanics models of molecular liquid systems is a problem of great practical and fundamental importance. Site-density functional theory (SDFT) is one of the promising directions in this area, but its success hinges upon the ability to efficiently reconcile the co-existence of two distinct intra- and inter-molecular interaction regimes in a molecular liquid. The renormalized formulation of SDFT (RSDFT), which we have recently developed, resolves this problem by introducing an additional potential field variable that decouples two interaction scales and maps the molecular liquid problem onto the effective simple liquid mixture. This work provides a critical assessment of RSDFT for the hydrated ion system-a problem that historically has always been one of the most difficult cases for SDFT applications. Using a two-site model of water, we perform a comprehensive analysis of hydrated alkali metal and halogen ions, including both structural and free energy based characteristics. The results indicate that RSDFT provides a significant improvement over conventional three-dimensional reference interaction site model implementations and may prove useful in coarse grained simulations based on two-site solvent models.
Collapse
Affiliation(s)
- Gennady N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Marat Valiev
- Molecular Sciences Software Group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| |
Collapse
|
9
|
Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Accurate prediction of hydration free energies and solvation structures using molecular density functional theory with a simple bridge functional. J Chem Phys 2021; 155:024117. [PMID: 34266282 DOI: 10.1063/5.0057506] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This paper assesses the ability of molecular density functional theory to predict efficiently and accurately the hydration free energies of molecular solutes and the surrounding microscopic water structure. A wide range of solutes were investigated, including hydrophobes, water as a solute, and the FreeSolv database containing 642 drug-like molecules having a variety of shapes and sizes. The usual second-order approximation of the theory is corrected by a third-order, angular-independent bridge functional. The overall functional is parameter-free in the sense that the only inputs are bulk water properties, independent of the solutes considered. These inputs are the direct correlation function, compressibility, liquid-gas surface tension, and excess chemical potential of the solvent. Compared to molecular simulations with the same force field and the same fixed solute geometries, the present theory is shown to describe accurately the solvation free energy and structure of both hydrophobic and hydrophilic solutes. Overall, the method yields a precision of order 0.5 kBT for the hydration free energies of the FreeSolv database, with a computer speedup of 3 orders of magnitude. The theory remains to be improved for a better description of the H-bonding structure and the hydration free energy of charged solutes.
Collapse
Affiliation(s)
- Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- Universié Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| |
Collapse
|
10
|
Miyata T, Yabuki N, Leung J. Transferability of Sigma Enlarging Bridge Function for Lennard-Jones Diatomic Solute Using Monatomic Solvent Correlation Obtained from Molecular Dynamics Simulation. CHEM LETT 2020. [DOI: 10.1246/cl.200521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tatsuhiko Miyata
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| | - Naoya Yabuki
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| | - Jackie Leung
- Department of Physics, Ehime University, 2-5 Bunkyo-Cho, Matsuyama, Ehime 790-8577, Japan
| |
Collapse
|
11
|
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]
|
12
|
Borgis D, Luukkonen S, Belloni L, Jeanmairet G. Simple Parameter-Free Bridge Functionals for Molecular Density Functional Theory. Application to Hydrophobic Solvation. J Phys Chem B 2020; 124:6885-6893. [DOI: 10.1021/acs.jpcb.0c04496] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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, PSL University, Sorbonne Université, CNRS, Paris, 75005, France
| | - Sohvi Luukkonen
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, 91191, France
| | - Guillaume Jeanmairet
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, Paris, F-75005, France
- Réseau sur le Stockage Électrochimique de l’Énergie, CNRS FR3459, 33 rue Saint Leu, Amiens, Cedex 80039, France
| |
Collapse
|
13
|
Zhang BW, Matubayasi N, Levy RM. Cavity Particle in Aqueous Solution with a Hydrophobic Solute: Structure, Energetics, and Functionals. J Phys Chem B 2020; 124:5220-5237. [PMID: 32469519 DOI: 10.1021/acs.jpcb.0c02721] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Endpoints density functional theory (DFT) provides a framework for calculating the excess chemical potential of a solute in solution using solvent distribution functions obtained from both physical endpoints of a hypothetical charging process which transforms the solvent density from that of the pure liquid to the solution state. In this work, the endpoints DFT equations are formulated in terms of the indirect (solvent-mediated) contribution ω(x) to the solute-solvent potential of mean force, and their connections are established with the conventional DFT expressions which are based on the use of direct correlation functions. ω actually corresponds to the free-energy cost to move a cavity particle (a tagged solvent molecule which interacts with the other solvent molecules but not the solute) from the bulk to the configuration x of a solvent molecule relative to the solute and is a suitable variable to describe the solvent effects on the solute-solvent interactions. HNC and PY type approximations are then used to integrate the DFT charging integral involved in the exact expression for the excess chemical potential. With these approximations, molecular simulations are to be performed at the two endpoints of solute insertion: pure solvent without the solute and the solution system with the fully coupled solute-solvent interaction. An endpoints method thus utilizes the ensembles of intermolecular configurations of physical interest, which are often readily accessible with MD simulations given the present computational power. To illustrate properties of the formulation, we perform simulations of model systems consisting of a cavity particle in an aqueous solution containing a spherical hydrophobic solute of three different sizes from which ω(x) and the solute chemical potential can be calculated using endpoints DFT expressions. These are compared with corresponding results obtained using the approximations needed in order to evaluate the endpoints DFT charging integral when cavity particle simulation data is not available. We analyze a new approximation (two-points quadratic HNC) to the DFT charging integral which captures the correct behavior of the cavity distributions at both endpoints of the solute insertion. The behavior of the cavity particle in simple and complex liquids plays an important role in various theoretical treatments of the solute chemical potential. For pure Lennard-Jones fluids, the free energy to bring a cavity particle from the bulk to the center of a fluid particle is negative. However, for solutes of varying size, this is not generally true for Lennard-Jones fluids or the systems studied in this work. We carry out energetic and structural analyses of the cavity particle in aqueous solution with hydrophobic solutes of varying size and discuss the results in the context of the hydrophobic effect.
Collapse
Affiliation(s)
- Bin W Zhang
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ronald M Levy
- Center for Biophysics and Computational Biology, and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Luukkonen S, Levesque M, Belloni L, Borgis D. Hydration free energies and solvation structures with molecular density functional theory in the hypernetted chain approximation. J Chem Phys 2020; 152:064110. [DOI: 10.1063/1.5142651] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Sohvi Luukkonen
- 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, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, 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, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| |
Collapse
|
16
|
Yamada K, Matubayasi N. Chain-Increment Method for Free-Energy Computation of a Polymer with All-Atom Molecular Simulations. Macromolecules 2020. [DOI: 10.1021/acs.macromol.9b01952] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuo Yamada
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
17
|
Matubayasi N. Energy-Representation Theory of Solutions: Its Formulation and Application to Soft, Molecular Aggregates. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20190246] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
18
|
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
| |
Collapse
|
19
|
Cao S, Konovalov KA, Unarta IC, Huang X. Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute–Solvent Interface. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Siqin Cao
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Kirill A. Konovalov
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Ilona Christy Unarta
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuhui Huang
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- HKUST‐Shenzhen Research Institute Hi‐Tech Park, Nanshan Shenzhen 518057 China
| |
Collapse
|
20
|
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
| |
Collapse
|
21
|
Masutani K, Yamamori Y, Kim K, Matubayasi N. Free-energy analysis of the hydration and cosolvent effects on the β-sheet aggregation through all-atom molecular dynamics simulation. J Chem Phys 2019; 150:145101. [DOI: 10.1063/1.5088395] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Keiichi Masutani
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Artificial Intelligence Research Center and Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo 135-0064, Japan
| | - Kang Kim
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
22
|
Urbic T. Two dimensional fluid with one site-site associating point. Monte Carlo, integral equation and thermodynamic perturbation theory study. J Mol Liq 2018; 270:87-96. [PMID: 30546180 DOI: 10.1016/j.molliq.2017.12.111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this paper we propose a model for the two dimensional fluid with one site-site associating point. We studied its structural and thermodynamic properties by the Monte Carlo computer simulations, the site-site integral equation theory (RISM), the Wertheim's thermodynamic perturbation theory (TPT) and the Wertheim's integral equation theory (WIET) for associative liquids. The model can have arbitrary position of the associating point from the center of particles. All particles have Lennard-Jones core while interactions between associating points are modeled as Gaussian like potential where the interaction depends only on the distance between sites. The methods were used to study the thermodynamic and structural properties as a function of the position of associating point, temperature and density. The accuracy of the analytic theories were checked by comparing the theoretical results with the corresponding Monte Carlo ones. The theories are quite accurate for cases when the associating point is on the surface and only dimers can be formed. In this case, the theories correctly predict the pair correlation functions of the model, internal energy, ratios of free and bonded particles and chemical potential. This is no longer true when associating point is away from the surface of particles and the higher clusters are formed.
Collapse
Affiliation(s)
- Tomaz Urbic
- University of Ljubljana, Department of Chemistry and Chemical Technology, Chair of Physical Chemistry, Večna pot 113, SI-1000 Ljubljana, Slovenia
| |
Collapse
|
23
|
Yamamoto N, Nakakuki I, Matubayasi N. Free-energy analysis of physisorption on solid-liquid interface with the solution theory in the energy representation. J Chem Phys 2018; 149:014504. [PMID: 29981552 DOI: 10.1063/1.5027861] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Physisorption of urea on its crystal in contact with water was subject to energetics analysis with all-atom molecular dynamics simulation. The transfer free energy of urea to an adsorption site was treated in the framework of the energy-representation theory of solutions, which allows a fast computation of the free energy in an inhomogeneous environment with solid-liquid interface. The preference of adsorption was then compared between the (001) and (110) faces, and it was found that the physisorption is more favorable on (001) than on (110) in correspondence to the hydrogen bonding between the adsorbed urea and the crystal urea. Among the terrace configurations of adsorption, the attractive interaction governs the preferable site with a minor role of the repulsive interaction. The effect of an edge was also treated by examining the terrace and step and was shown to be strongly operative on the (110) face when the CO group of the adsorbed urea points toward the edge. The present work demonstrates that the solution theory can be a framework for analyzing the energetics of physisorption and addressing the roles of the crystal and liquid at the interface through the systematic decomposition of free energy.
Collapse
Affiliation(s)
- Naoki Yamamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ippei Nakakuki
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
24
|
Kawakami T, Shigemoto I, Matubayasi N. Structure and permeability of ionomers studied by atomistic molecular simulation combined with the theory of solutions in the energy representation. J Chem Phys 2018; 148:214903. [PMID: 29884036 DOI: 10.1063/1.5018884] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ionomers play a key role in forming the catalyst layer of polymer electrolyte fuel cells. In the present work, we performed atomistic molecular dynamics simulations and free-energy calculations with the energy-representation method for sulfonated polyethersulfone (SPES) and its derivatives toward the rational design of ionomers for carbon alloy catalysts. It was observed that H2O aggregates strongly in the branched SPES systems with fluorocarbons and is located homogeneously in the systems without fluorocarbons. The O2 permeability was then examined within the framework of the solubility-diffusion mechanism. The permeability was seen to be large for the branched SPES with fluorocarbons, indicating that the performance of ionomers as a permeation medium for O2 may be tuned by the flexibility and branching of the polymer chain.
Collapse
Affiliation(s)
- Tomonori Kawakami
- Advanced Materials Research Laboratories, Toray Industries, Inc., 2-1 Sonoyama 3-chome, Otsu, Shiga 520-0842, Japan
| | - Isamu Shigemoto
- Advanced Materials Research Laboratories, Toray Industries, Inc., 2-1 Sonoyama 3-chome, Otsu, Shiga 520-0842, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
25
|
Tokunaga Y, Yamamori Y, Matubayasi N. Probabilistic analysis for identifying the driving force of protein folding. J Chem Phys 2018; 148:125101. [PMID: 29604891 DOI: 10.1063/1.5019410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.
Collapse
Affiliation(s)
- Yoshihiko Tokunaga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| |
Collapse
|
26
|
Ansari SM, Palmer DS. Comparative Molecular Field Analysis Using Molecular Integral Equation Theory. J Chem Inf Model 2018; 58:1253-1265. [DOI: 10.1021/acs.jcim.7b00600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samiul M. Ansari
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| | - David S. Palmer
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, U.K
| |
Collapse
|
27
|
Mizuguchi T, Matubayasi N. Free-Energy Analysis of Peptide Binding in Lipid Membrane Using All-Atom Molecular Dynamics Simulation Combined with Theory of Solutions. J Phys Chem B 2018; 122:3219-3229. [DOI: 10.1021/acs.jpcb.7b08241] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomoko Mizuguchi
- Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan
- Institute for the Promotion of University Strategy, Kyoto Institute of Technology, Kyoto 606-8585, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
28
|
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
| |
Collapse
|
29
|
Correction of Kovalenko-Hirata closure in Ornstein-Zernike integral equation theory for Lennard-Jones fluids. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.05.134] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
30
|
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
| |
Collapse
|
31
|
Yamamori Y, Matubayasi N. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. J Chem Phys 2017; 146:225103. [DOI: 10.1063/1.4985222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
32
|
Harris RC, Deng N, Levy RM, Ishizuka R, Matubayasi N. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points. J Comput Chem 2016; 38:1198-1208. [PMID: 28008630 DOI: 10.1002/jcc.24668] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/02/2016] [Accepted: 10/26/2016] [Indexed: 01/17/2023]
Abstract
Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Robert C Harris
- Department of Chemistry and Center for Biophysics and Computational Biology and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122
| | - Nanjie Deng
- Department of Chemistry and Center for Biophysics and Computational Biology and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122.,Department of Chemistry and Physical Sciences, Dyson College of Arts and Sciences, Pace University, New York, New York, 10038
| | - Ronald M Levy
- Department of Chemistry and Center for Biophysics and Computational Biology and Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
| |
Collapse
|
33
|
Urbic T. Properties of the two-dimensional heterogeneous Lennard-Jones dimers: An integral equation study. J Chem Phys 2016; 145:194503. [PMID: 27875894 PMCID: PMC5116027 DOI: 10.1063/1.4967807] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/02/2016] [Indexed: 11/14/2022] Open
Abstract
Structural and thermodynamic properties of a planar heterogeneous soft dumbbell fluid are examined using Monte Carlo simulations and integral equation theory. Lennard-Jones particles of different sizes are the building blocks of the dimers. The site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions and the thermodynamic properties. Obtained results are compared to Monte Carlo simulation data. The critical parameters for selected types of dimers were also estimated and the influence of the Lennard-Jones parameters was studied. We have also tested the correctness of the site-site integral equation theory using different closures.
Collapse
Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Vecna pot 113, 1000 Lubljana, Slovenia
| |
Collapse
|
34
|
Matubayasi N. Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions. Curr Opin Struct Biol 2016; 43:45-54. [PMID: 27835803 DOI: 10.1016/j.sbi.2016.10.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/07/2016] [Indexed: 11/25/2022]
Abstract
The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics.
Collapse
Affiliation(s)
- Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan.
| |
Collapse
|
35
|
Borówko M, Rżysko W, Sokołowski S, Staszewski T. Integral equations theory for two-dimensional systems involving nanoparticles. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1234079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Małgorzata Borówko
- Department for the Modeling of Physico-Chemical Processes, Maria Curie-Skłodowska University, Lublin, Poland
| | - Wojciech Rżysko
- Department for the Modeling of Physico-Chemical Processes, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stefan Sokołowski
- Department for the Modeling of Physico-Chemical Processes, Maria Curie-Skłodowska University, Lublin, Poland
| | - Tomasz Staszewski
- Department for the Modeling of Physico-Chemical Processes, Maria Curie-Skłodowska University, Lublin, Poland
| |
Collapse
|
36
|
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
|
37
|
Yamamori Y, Ishizuka R, Karino Y, Sakuraba S, Matubayasi N. Interaction-component analysis of the hydration and urea effects on cytochrome c. J Chem Phys 2016; 144:085102. [DOI: 10.1063/1.4941945] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yasuhito Karino
- RIKEN Quantitative Biology Center, Kobe, Hyogo 650-0047, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8568, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| |
Collapse
|
38
|
Sergiievskyi V, Jeanmairet G, Levesque M, Borgis D. Solvation free-energy pressure corrections in the three dimensional reference interaction site model. J Chem Phys 2015; 143:184116. [DOI: 10.1063/1.4935065] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
|
39
|
Kamo F, Ishizuka R, Matubayasi N. Correlation analysis for heat denaturation of Trp-cage miniprotein with explicit solvent. Protein Sci 2015; 25:56-66. [PMID: 26189564 DOI: 10.1002/pro.2754] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/15/2015] [Indexed: 11/10/2022]
Abstract
Energetics was analyzed for Trp-cage miniprotein in water to elucidate the solvation effect in heat denaturation. The solvation free energy was computed for a set of protein structures at room and high temperatures with all-atom molecular dynamics simulation combined with the solution theory in the energy representation, and its correlations were investigated against the intramolecular (structural) energy of the protein and the average interaction energy of the protein with the solvent water. It was observed both at room and high temperatures that the solvation free energy is anticorrelated to the structural energy and varies in parallel to the electrostatic component of the protein-water interaction energy without correlations to the van der Waals and excluded-volume components. When the set of folded structures sampled at room temperature was compared with the set of unfolded ones at high temperature, it was found that the preference order of the two sets is in correspondence to the van der Waals and excluded-volume components in the sum of the protein intramolecular and protein-water intermolecular interactions and is not distinguished by the electrostatic component.
Collapse
Affiliation(s)
- Fumitaka Kamo
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan
| | - Ryosuke Ishizuka
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, 560-8531, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, 615-8520, Japan
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
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
| |
Collapse
|
42
|
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
| |
Collapse
|
43
|
Ishizuka R, Matubayasi N, Tu KM, Umebayashi Y. Energetic Contributions from the Cation and Anion to the Stability of Carbon Dioxide Dissolved in Imidazolium-Based Ionic Liquids. J Phys Chem B 2015; 119:1579-87. [DOI: 10.1021/jp5101957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryosuke Ishizuka
- Division
of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Nobuyuki Matubayasi
- Division
of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- Elements
Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Kai-Min Tu
- Department
of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Kyoto 606-8502, Japan
| | - Yasuhiro Umebayashi
- Graduate
School of Science and Technology, Niigata University, 8050, Ikarashi
2-no-cho, Nisi-ku, Niigata 950-2181, Japan
| |
Collapse
|
44
|
Li B, Matveev AV, Krüger S, Rösch N. Uranyl solvation by a reference interaction site model. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.10.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
45
|
Titov SV. Discrete models for describing photophysical and thermodynamic properties of polar liquids. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s003602441411017x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
46
|
Sakuraba S, Matubayasi N. Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions. J Comput Chem 2014; 35:1592-608. [DOI: 10.1002/jcc.23651] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/10/2014] [Accepted: 05/16/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Shun Sakuraba
- Quantum Beam Science Directorate, Japan Atomic Energy Agency; Kizugawa Kyoto 619-0215 Japan
- Institute for Molecular Science; Okazaki Aichi 444-8585 Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering; Graduate School of Engineering Science; Osaka University; Toyonaka Osaka 560-8531 Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University; Katsura Kyoto 615-8520 Japan
- Japan Science and Technology Agency (JST), CREST; Kawaguchi Saitama 332-0012 Japan
| |
Collapse
|
47
|
Sergiievskyi VP, Jeanmairet G, Levesque M, Borgis D. Fast Computation of Solvation Free Energies with Molecular Density Functional Theory: Thermodynamic-Ensemble Partial Molar Volume Corrections. J Phys Chem Lett 2014; 5:1935-1942. [PMID: 26273876 DOI: 10.1021/jz500428s] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular density functional theory (MDFT) offers an efficient implicit-solvent method to estimate molecule solvation free-energies, whereas conserving a fully molecular representation of the solvent. Even within a second-order approximation for the free-energy functional, the so-called homogeneous reference fluid approximation, we show that the hydration free-energies computed for a data set of 500 organic compounds are of similar quality as those obtained from molecular dynamics free-energy perturbation simulations, with a computer cost reduced by 2-3 orders of magnitude. This requires to introduce the proper partial volume correction to transform the results from the grand canonical to the isobaric-isotherm ensemble that is pertinent to experiments. We show that this correction can be extended to 3D-RISM calculations, giving a sound theoretical justification to empirical partial molar volume corrections that have been proposed recently.
Collapse
Affiliation(s)
- Volodymyr P Sergiievskyi
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Guillaume Jeanmairet
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Maximilien Levesque
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
| | - Daniel Borgis
- †École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris, France
- ‡Maison de la Simulation, CNRS USR 3441, CEA Saclay, 91191 Gif-sur-Yvette, France
| |
Collapse
|
48
|
Urbic T, Dias CL. Properties of the Lennard-Jones dimeric fluid in two dimensions: an integral equation study. J Chem Phys 2014; 140:094703. [PMID: 24606372 PMCID: PMC3977749 DOI: 10.1063/1.4867289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 02/19/2014] [Indexed: 12/21/2022] Open
Abstract
The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.
Collapse
Affiliation(s)
- Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Aškerčeva 5, SI-1000 Ljubljana, Slovenia
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, USA
| |
Collapse
|
49
|
Palmer DS, Sørensen J, Schiøtt B, Fedorov MV. Solvent Binding Analysis and Computational Alanine Scanning of the Bovine Chymosin–Bovine κ-Casein Complex Using Molecular Integral Equation Theory. J Chem Theory Comput 2013; 9:5706-17. [DOI: 10.1021/ct400605x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David S. Palmer
- Department
of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| | - Jesper Sørensen
- Department
of Chemistry and Biochemistry, University of California, San Diego, Urey Hall, 9500 Gilman Drive, La Jolla, California 92093, United States
- The
Center for Insoluble Protein Structures (inSPIN) and the Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Birgit Schiøtt
- The
Center for Insoluble Protein Structures (inSPIN) and the Interdisciplinary
Nanoscience Center (iNANO), Department of Chemistry, Aarhus University, Langelandsgade
140, DK-8000 Aarhus
C, Denmark
| | - Maxim V. Fedorov
- Department
of Physics, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow, Scotland G4 0NG, United Kingdom
- Max Planck Institute for Mathematics in the Sciences, Inselstrasse 22, DE-04103 Leipzig, Germany
| |
Collapse
|
50
|
Anashkin IP, Klinov AV. Determining the parameters of the potential of intermolecular interaction by the Zeno line. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413110034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|