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Kalyuzhnyi YV, Patsahan T, Holovko M, Cummings PT. Phase behavior of patchy colloids confined in patchy porous media. NANOSCALE 2024; 16:4668-4677. [PMID: 38305436 DOI: 10.1039/d3nr02866f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
A simple model for functionalized disordered porous media is proposed and the effects of confinement on self-association, percolation and phase behavior of a fluid of patchy particles are studied. The media are formed by randomly distributed hard-sphere obstacles fixed in space and decorated by a certain number of off-center square-well sites. The properties of the fluid of patchy particles, represented by the fluid of hard spheres each bearing a set of the off-center square-well sites, are studied using an appropriate combination of the scaled particle theory for the porous media, Wertheim's thermodynamic perturbation theory, and Flory-Stockmayer theory. To assess the accuracy of the theory a set of computer simulations have been performed. In general, predictions of the theory appeared to be in good agreement with the computer simulation results. Confinement and competition between the formation of bonds connecting the fluid particles, and connecting fluid particles and obstacles of the matrix, gave rise to a re-entrant phase behavior with three critical points and two separate regions of the liquid-gas phase coexistence.
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Affiliation(s)
- Yurij V Kalyuzhnyi
- Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii Street, UA-79011 Lviv, Ukraine.
| | - Taras Patsahan
- Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii Street, UA-79011 Lviv, Ukraine.
- Lviv Polytechnic National University, 12 S. Bandera Street, UA-79013 Lviv, Ukraine
| | - Myroslav Holovko
- Institute for Condensed Matter Physics of the National Academy of Sciences of Ukraine, 1 Svientsitskii Street, UA-79011 Lviv, Ukraine.
| | - Peter T Cummings
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK
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2
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Nguyen DV, Hengphasatporn K, Danova A, Suroengrit A, Boonyasuppayakorn S, Fujiki R, Shigeta Y, Rungrotmongkol T, Chavasiri W. Structure-yeast α-glucosidase inhibitory activity relationship of 9-O-berberrubine carboxylates. Sci Rep 2023; 13:18865. [PMID: 37914757 PMCID: PMC10620162 DOI: 10.1038/s41598-023-45116-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Thirty-five 9-O-berberrubine carboxylate derivatives were synthesized and evaluated for yeast α-glucosidase inhibitory activity. All compounds demonstrated better inhibitory activities than the parent compounds berberine (BBR) and berberrubine (BBRB), and a positive control, acarbose. The structure-activity correlation study indicated that most of the substituents on the benzoate moiety such as methoxy, hydroxy, methylenedioxy, benzyloxy, halogen, trifluoromethyl, nitro and alkyl can contribute to the activities except multi-methoxy, fluoro and cyano. In addition, replacing benzoate with naphthoate, cinnamate, piperate or diphenylacetate also led to an increase in inhibitory activities except with phenyl acetate. 9, 26, 27, 28 and 33 exhibited the most potent α-glucosidase inhibitory activities with the IC50 values in the range of 1.61-2.67 μM. Kinetic study revealed that 9, 26, 28 and 33 interacted with the enzyme via competitive mode. These four compounds were also proved to be not cytotoxic at their IC50 values. The competitive inhibition mechanism of these four compounds against yeast α-glucosidase was investigated using molecular docking and molecular dynamics simulations. The binding free energy calculations suggest that 26 exhibited the strongest binding affinity, and its binding stability is supported by hydrophobic interactions with D68, F157, F158 and F177. Therefore, 9, 26, 28 and 33 would be promising candidates for further studies of antidiabetic activity.
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Affiliation(s)
- Duy Vu Nguyen
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Ade Danova
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand
- Organic Chemistry Division, Department of Chemistry, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
| | - Aphinya Suroengrit
- Department of Microbiology, Faculty of Medicine, Center of Excellence in Applied Medical Virology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Siwaporn Boonyasuppayakorn
- Department of Microbiology, Faculty of Medicine, Center of Excellence in Applied Medical Virology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ryo Fujiki
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Thanyada Rungrotmongkol
- Bioinformatics and Computational Biology Program, Graduated School, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Biochemistry, Faculty of Science, Center of Excellence in Biocatalyst and Sustainable Biotechnology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Warinthorn Chavasiri
- Department of Chemistry, Faculty of Science, Center of Excellence in Natural Products Chemistry, Chulalongkorn University, Pathumwan, Bangkok, 10330, Thailand.
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Cao S, Kalin ML, Huang X. EPISOL: A software package with expanded functions to perform 3D-RISM calculations for the solvation of chemical and biological molecules. J Comput Chem 2023; 44:1536-1549. [PMID: 36856731 DOI: 10.1002/jcc.27088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/24/2022] [Accepted: 01/29/2023] [Indexed: 03/02/2023]
Abstract
Integral equation theory (IET) provides an effective solvation model for chemical and biological systems that balances computational efficiency and accuracy. We present a new software package, the expanded package for IET-based solvation (EPISOL), that performs 3D-reference interaction site model (3D-RISM) calculations to obtain the solvation structure and free energies of solute molecules in different solvents. In EPISOL, we have implemented 22 different closures, multiple free energy functionals, and new variations of 3D-RISM theory, including the recent hydrophobicity-induced density inhomogeneity (HI) theory for hydrophobic solutes and ion-dipole correction (IDC) theory for negatively charged solutes. To speed up the convergence and enhance the stability of the self-consistent iterations, we have introduced several numerical schemes in EPISOL, including a newly developed dynamic mixing approach. We show that these schemes have significantly reduced the failure rate of 3D-RISM calculations compared to AMBER-RISM software. EPISOL consists of both a user-friendly graphic interface and a kernel library that allows users to call its routines and adapt them to other programs. EPISOL is compatible with the force-field and coordinate files from both AMBER and GROMACS simulation packages. Moreover, EPISOL is equipped with an internal memory control to efficiently manage the use of physical memory, making it suitable for performing calculations on large biomolecules. We demonstrate that EPISOL can efficiently and accurately calculate solvation density distributions around various solute molecules (including a protein chaperone consisting of 120,715 atoms) and obtain solvent free energy for a wide range of organic compounds. We expect that EPISOL can be widely applied as a solvation model for chemical and biological systems. EPISOL is available at https://github.com/EPISOLrelease/EPISOL.
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Affiliation(s)
- Siqin Cao
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael L Kalin
- Biophysics Graduate Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Cao S, Qiu Y, Unarta IC, Goonetilleke EC, Huang X. The Ion-Dipole Correction of the 3DRISM Solvation Model to Accurately Compute Water Distributions around Negatively Charged Biomolecules. J Phys Chem B 2022; 126:8632-8645. [PMID: 36282904 DOI: 10.1021/acs.jpcb.2c04431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The 3D reference interaction site model (3DRISM) provides an efficient grid-based solvation model to compute the structural and thermodynamic properties of biomolecules in aqueous solutions. However, it remains challenging for existing 3DRISM methods to correctly predict water distributions around negatively charged solute molecules. In this paper, we first show that this challenge is mainly due to the orientation of water molecules in the first solvation shell of the negatively charged solute molecules. To properly consider this orientational preference, position-dependent two-body intramolecular correlations of solvent need to be included in the 3DRISM theory, but direct evaluations of these position-dependent two-body intramolecular correlations remain numerically intractable. To address this challenge, we introduce the Ion-Dipole Correction (IDC) to the 3DRISM theory, in which we incorporate the orientation preference of water molecules via an additional solute-solvent interaction term (i.e., the ion-dipole interaction) while keeping the formulism of the 3DRISM equation unchanged. We prove that this newly introduced IDC term is equivalent to an effective direct correlation function which can effectively consider the orientation effect that arises from position dependent two-body correlations. We first quantitatively validate our 3DRISM-IDC theory combined with the PSE3 closure on Cl-, [ClO]- (a two-site anion), and [NO2]- (a three-site anion). For all three anions, we show that our 3DRISM-IDC theory significantly outperforms the 3DRISM theory in accurately predicting the solvation structures in comparison to MD simulations, including RDFs and 3D water distributions. Furthermore, we have also demonstrated that the 3DRISM-IDC can improve the accuracy of hydration free-energy calculation for Cl-. We further demonstrate that our 3DRISM-IDC theory yields significant improvements over the 3DRISM theory when applied to compute the solvation structures for various negatively charged solute molecules, including adenosine triphosphate (ATP), a short peptide containing 19 residues, a DNA hairpin containing 24 nucleotides, and a riboswitch RNA molecule with 77 nucleotides. We expect that our 3DRISM-IDC-PSE3 solvation model holds great promise to be widely applied to study solvation properties for nucleic acids and other biomolecules containing negatively charged functional groups.
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Affiliation(s)
- Siqin Cao
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Yunrui Qiu
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Ilona C Unarta
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Eshani C Goonetilleke
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
| | - Xuhui Huang
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin53706, United States
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5
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Nelson A, Kalyuzhnyi Y, Patsahan T, McCabe C. Liquid-vapor phase equilibrium of a simple liquid confined in a random porous media: Second-order Barker-Henderson perturbation theory and scaled particle theory. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112348] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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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
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7
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Wang N, Huang X, Gong H, Zhou Y, Li X, Li F, Bao Y, Xie C, Wang Z, Yin Q, Hao H. Thermodynamic mechanism of selective cocrystallization explored by MD simulation and phase diagram analysis. AIChE J 2019. [DOI: 10.1002/aic.16570] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Na Wang
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Xin Huang
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Hao Gong
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
- Key Laboratory for Green Chemical Technology of Ministry of Education, R&D Center for Petrochemical TechnologyTianjin University Tianjin China
| | - Yanan Zhou
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Xin Li
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Fei Li
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
| | - Ying Bao
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Chuang Xie
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Zhao Wang
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Qiuxiang Yin
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
| | - Hongxun Hao
- National Engineering Research Center of Industrial Crystallization TechnologySchool of Chemical Engineering and Technology, Tianjin University Tianjin China
- Collaborative Innovation Center of Chemical Science and Engineering Tianjin China
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8
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Qiao CZ, Zhao SL, Liu HL, Dong W. Fluids in porous media. IV. Quench effect on chemical potential. J Chem Phys 2017. [PMID: 28641429 DOI: 10.1063/1.4984773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
It appears to be a common sense to measure the crowdedness of a fluid system by the densities of the species constituting it. In the present work, we show that this ceases to be valid for confined fluids under some conditions. A quite thorough investigation is made for a hard sphere (HS) fluid adsorbed in a hard sphere matrix (a quench-annealed system) and its corresponding equilibrium binary mixture. When fluid particles are larger than matrix particles, the quench-annealed system can appear much more crowded than its corresponding equilibrium binary mixture, i.e., having a much higher fluid chemical potential, even when the density of each species is strictly the same in both systems, respectively. We believe that the insight gained from this study should be useful for the design of functionalized porous materials.
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Affiliation(s)
- C Z Qiao
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Université Lyon 1, Laboratoire de Chimie, UMR 5182, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
| | - S L Zhao
- School of Chemical Engineering and State Key Laboratory of Chemical Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, China
| | - H L Liu
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Road, 200237 Shanghai, China
| | - W Dong
- Université de Lyon, CNRS, Ecole Normale Supérieure de Lyon, Université Lyon 1, Laboratoire de Chimie, UMR 5182, 46, Allée d'Italie, 69364 Lyon Cedex 07, France
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Jadrich RB, Schweizer KS. Directing colloidal assembly and a metal-insulator transition using a quench-disordered porous rod template. PHYSICAL REVIEW LETTERS 2014; 113:208302. [PMID: 25432057 DOI: 10.1103/physrevlett.113.208302] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Indexed: 06/04/2023]
Abstract
Replica and effective-medium theory methods are employed to elucidate how to massively reconfigure a colloidal assembly to achieve globally homogeneous, strongly clustered, and percolated equilibrium states of high electrical conductivity at low physical volume fractions. A key idea is to employ a quench-disordered, large-mesh rigid-rod network as a templating internal field. By exploiting bulk phase separation frustration and the tunable competing processes of colloid adsorption on the low-dimensional network and fluctuation-driven colloid clustering in the pore spaces, two distinct spatial organizations of greatly enhanced particle contacts can be achieved. As a result, a continuous, but very abrupt, transition from an insulating to metallic-like state can be realized via a small change of either the colloid-template or colloid-colloid attraction strength. The approach is generalizable to more complicated template or colloidal architectures.
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Affiliation(s)
- Ryan B Jadrich
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA and Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, USA
| | - Kenneth S Schweizer
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA and Department of Materials Science, University of Illinois, Urbana, Illinois 61801, USA and Frederick Seitz Materials Research Laboratory, University of Illinois, Urbana, Illinois 61801, USA
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10
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Multiscale modeling of solvation in chemical and biological nanosystems and in nanoporous materials. PURE APPL CHEM 2013. [DOI: 10.1351/pac-con-12-06-03] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Statistical–mechanical, 3D-RISM-KH molecular theory of solvation (3D reference interaction site model with the Kovalenko–Hirata closure) is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. 3D-RISM-KH explains the molecular mechanisms of self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), aggregation of prion proteins and β-sheet amyloid oligomers, protein-ligand binding, and function-related solvation properties of complexes as large as the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) and GroEL/ES chaperone. Molecular mechanics/Poisson–Boltzmann (generalized Born) surface area [MM/PB(GB)SA] post-processing of molecular dynamics (MD) trajectories involving SA empirical nonpolar terms is replaced with MM/3D-RISM-KH statistical–mechanical evaluation of the solvation thermodynamics. 3D-RISM-KH has been coupled with multiple time-step (MTS) MD of the solute biomolecule driven by effective solvation forces, which are obtained analytically by converging the 3D-RISM-KH integral equations at outer time-steps and are calculated in between by using solvation force coordinate extrapolation (SFCE) in the subspace of previous solutions to 3D-RISM-KH. The procedure is stabilized by the optimized isokinetic Nosé–Hoover (OIN) chain thermostatting, which enables gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties. The multiscale OIN/SFCE/3D-RISM-KH algorithm is implemented in the Amber package and illustrated on a fully flexible model of alanine dipeptide in aqueous solution, exhibiting the computational rate of solvent sampling 20 times faster than standard MD with explicit solvent. Further substantial acceleration can be achieved with 3D-RISM-KH efficiently sampling essential events with rare statistics such as exchange and localization of solvent, ions, and ligands at binding sites and pockets of the biomolecule. 3D-RISM-KH was coupled with ab initio complete active space self-consistent field (CASSCF) and orbital-free embedding (OFE) Kohn–Sham (KS) density functional theory (DFT) quantum chemistry methods in an SCF description of electronic structure, optimized geometry, and chemical reactions in solution. The (OFE)KS-DFT/3D-RISM-KH multi-scale method is implemented in the Amsterdam Density Functional (ADF) package and extensively validated against experiment for solvation thermochemistry, photochemistry, conformational equilibria, and activation barriers of various nanosystems in solvents and ionic liquids (ILs). Finally, the replica RISM-KH-VM molecular theory for the solvation structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous materials reveals the molecular mechanisms of sorption and supercapacitance in nanoporous carbon electrodes, which is drastically different from a planar electrical double layer.
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11
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Sato H. A modern solvation theory: quantum chemistry and statistical chemistry. Phys Chem Chem Phys 2013; 15:7450-65. [DOI: 10.1039/c3cp50247c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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KOVALENKO ANDRIY, HIRATA FUMIO. TOWARDS A MOLECULAR THEORY FOR THE VAN DER WAALS–MAXWELL DESCRIPTION OF FLUID PHASE TRANSITIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633602000282] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We briefly review developments of theories for phase transitions of molecular fluids and mixtures, from semi-phenomenological approaches providing equations of state with adjustable parameters to first-principles microscopic methods qualitatively correct for a variety of molecular models with realistic interaction potentials. We further present the generalization of the van der Waals–Maxwell description of fluid phase diagrams to account for chemical specificities of polar molecular fluids, such as hydrogen bonding. Our theory uses the reference interaction site model (RISM) integral equation approach complemented with the new closure we have proposed (KH approximation), successful over a wide range of density from gas to liquid. The RISM/KH theory is applied to the known three-site models of water, methanol, and hydrogen fluoride. It qualitatively reproduces their vapor-liquid phase diagrams and the structure in the gas as well as liquid phases, including hydrogen bonding. Furthermore, phase transitions of water and methanol sorbed in nanoporous carbon aerogel are described by means of the replica generalization of the RISM approach we have developed. The changes as compared to the bulk fluids are in agreement with simulations and experiment. The RISM/KH theory is promising for description of phase transitions in various associating fluids, in particular, electrolyte as well as non-electrolyte solutions and ionic liquids.
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Affiliation(s)
- ANDRIY KOVALENKO
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - FUMIO HIRATA
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
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13
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Woelki S, Bari Bhuiyan L, Henderson D. Application of the singlet reference interaction site model to the primitive model double layer. Mol Phys 2011. [DOI: 10.1080/00268976.2010.530302] [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]
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14
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Ishizuka R, Chong SH, Hirata F. An integral equation theory for inhomogeneous molecular fluids: the reference interaction site model approach. J Chem Phys 2008; 128:034504. [PMID: 18205507 DOI: 10.1063/1.2819487] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An integral equation theory which is applicable to inhomogeneous molecular liquids is proposed. The "inhomogeneous reference interaction site model (RISM)" equation derived here is a natural extension of the RISM equation to inhomogeneous systems. This theory makes it possible to calculate the pair correlation function between two molecules which are located at different density regions. We also propose approximations concerning the closure relation and the intramolecular susceptibility of inhomogeneous molecular liquids. As a preliminary application of the theory, the hydration structure around an ion is investigated. Lithium, sodium, and potassium cations are chosen as the solute. Using the Percus trick, the local density of solvent around an ion is expressed in terms of the solute-solvent pair correlation function calculated from the RISM theory. We then analyze the hydration structure around an ion through the triplet correlation function which is defined with the inhomogeneous pair correlation function and the local density of the solvent. The results of the triplet correlation functions for cations indicate that the thermal fluctuation of the hydration shell is closely related to the size of the solute ion. The triplet correlation function from the present theory is also compared with that from the Kirkwood superposition approximation, which substitutes the inhomogeneous pair correlation by the homogeneous one. For the lithium ion, the behavior of the triplet correlation functions from the present theory shows marked differences from the one calculated within the Kirkwood approximation.
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Affiliation(s)
- R Ishizuka
- Department of Theoretical Molecular Science, Institute for Molecular Science, Okazaki 444-8585, Japan
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15
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Sarkisov L. Theory of pair connectedness in templated quenched-annealed systems. J Chem Phys 2008; 128:044707. [DOI: 10.1063/1.2823734] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Woelki S, Kohler HH, Krienke H, Schmeer G. Improvements of DRISM calculations: symmetry reduction and hybrid algorithms. Phys Chem Chem Phys 2008; 10:898-910. [DOI: 10.1039/b712306j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Tanimura A, Kovalenko A, Hirata F. Structure of electrolyte solutions sorbed in carbon nanospaces, studied by the replica RISM theory. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:1507-17. [PMID: 17241081 DOI: 10.1021/la061617i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The replica RISM theory is used to investigate the structure of electrolyte solutions confined in carbonized polyvinylidene chloride (PVDC) nanoporous material, compared to bulk electrolyte solution. Comparisons are made between the models of electrolyte solution sorbed in the carbonized PVDC material and a single carbon nanosphere in bulk electrolyte solution. Particular attention is paid to the chemical potential balance between the species of the sorbed electrolyte solution and the bulk solution in contact with the nanoporous material. As a result of the strong hydrophobicity of the carbonized PVDC material in the absence of activating chemical groups, the densities of water and ions sorbed in the material are remarkably low compared to those in the ambient bulk solution. The interaction between water molecules and cations becomes strong in nanospaces. It turns out that, in carbon nanopores, a cation adsorbed at the carbon surface is fully surrounded by the hydration shell of water molecules which separates the cation and the surface. Distinctively, an anion is adsorbed in direct contact with the carbon surface, which squeezes a part of its hydration shell out. The tendency increases toward smaller cations, which are characterized as "positive hydration" ions. In the bulk, cations are not hydrated so strongly and behave similarly to anions. The results suggest that the specific capacitance of an electric double-layer supercapacitor with nanoporous electrodes is intimately related to the solvation structure of electrolyte solution sorbed in nanopores, which is affected by the microscopic structure of the nanoporous electrode.
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Affiliation(s)
- A Tanimura
- Institute for Molecular Science, Okazaki 444-8585, Japan
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18
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Abstract
The morphology of many porous materials is spongelike. Despite the abundance of such materials, simple models which allow for a theoretical description of these materials are still lacking. Here, we propose a hard sponge model which is made by digging spherical cavities in a solid continuum. We found an analytical expression for describing the interaction potential between fluid particles and the spongelike porous matrix. The diagrammatic expansions of different correlation functions are derived as well as that of grand potential. We derived also the Ornstein-Zernike (OZ) equations for this model. In contrast to Madden-Glandt model of random porous media [W. G. Madden and E. D. Glandt, J. Stat. Phys. 51, 537 (1988)], the OZ equations for a fluid confined in our hard sponge model have some similarity to the OZ equations of a three-component fluid mixture. We show also how the replica method can be extended to study our sponge model and that the same OZ equations can be derived also from the extended replica method.
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Affiliation(s)
- S L Zhao
- School of Theoretical Physics and School of Material Science and Engineering, Hunan University, Changsha, 410082, China
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19
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Sarkisov L, Van Tassel PR. Replica Ornstein-Zernike theory of adsorption in a templated porous material: Interaction site systems. J Chem Phys 2005; 123:164706. [PMID: 16268721 DOI: 10.1063/1.2049247] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Molecular templating offers the possibility of porous materials whose selectivity rivals the molecular recognition observed in nature. The design of templated materials requires a molecular understanding of the templating effect on the material structure and performance. We present here a theoretical description of adsorption in a model templated porous material. Our model material is a quenched, equilibrated mixture of template and matrix molecular species where the template component has been subsequently removed. We propose a set of site-site [i.e., reference interaction site model (RISM)] replica Ornstein-Zernike equations relating the correlation functions of template, matrix, and adsorbing fluid molecules. To test this approach, we focus here on systems interacting via hard-sphere site-site potentials and employ a Percus-Yevick closure. We consider chain and cluster species composed of up to five spheres and observe a range of effects associated with template structure, including higher affinity toward, and enhanced templating by, compact cluster molecules. We assess these effects by grand canonical Monte Carlo simulation and discuss their implication to the design of templated molecular recognition materials.
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Affiliation(s)
- Lev Sarkisov
- Department of Chemical Engineering, Yale University, New Haven, Connecticut 06520-8286, USA
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20
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Sung BJ, Yethiraj A. Monte Carlo simulation and self-consistent integral equation theory for polymers in quenched random media. J Chem Phys 2005; 123:074909. [PMID: 16229622 DOI: 10.1063/1.2008232] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The conformational properties and static structure of freely jointed hard-sphere chains in matrices composed of stationary hard spheres are studied using Monte Carlo simulations and integral equation theory. The simulations show that the chain size is a nonmonotonic function of the matrix density when the matrix spheres are the same size as the monomers. When the matrix spheres are of the order of the chain size the chain size decreases monotonically with increasing matrix volume fraction. The simulations are used to test the replica-symmetric polymer reference interaction site model (RSP) integral equation theory. When the simulation results for the intramolecular correlation functions are input into the theory, the agreement between theoretical predictions and simulation results for the pair-correlation functions is quantitative only at the highest fluid volume fractions and for small matrix sphere sizes. The RSP theory is also implemented in a self-consistent fashion, i.e., the intramolecular and intermolecular correlation functions are calculated self-consistently by combining a field theory with the integral equations. The theory captures qualitative trends observed in the simulations, such as the nonmonotonic dependence of the chain size on media fraction.
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Affiliation(s)
- Bong June Sung
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Urbic T, Vlachy V, Pizio O, Dill K. Water-like fluid in the presence of Lennard–Jones obstacles: predictions of an associative replica Ornstein–Zernike theory. J Mol Liq 2004. [DOI: 10.1016/j.molliq.2003.12.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Matubayasi N, Nakahara M. Theory of solutions in the energy representation. III. Treatment of the molecular flexibility. J Chem Phys 2003. [DOI: 10.1063/1.1613938] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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23
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Tanimura A, Kovalenko A, Hirata F. Molecular theory of an electrochemical double layer in a nanoporous carbon supercapacitor. Chem Phys Lett 2003. [DOI: 10.1016/s0009-2614(03)01336-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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24
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Fernaud MJ, Lomba E, Martı́n C, Levesque D, Weis JJ. Study of dipolar fluid inclusions in charged random matrices. J Chem Phys 2003. [DOI: 10.1063/1.1576377] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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