1
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Maruyama Y, Yoshida N. RISMiCal: A software package to perform fast RISM/3D-RISM calculations. J Comput Chem 2024; 45:1470-1482. [PMID: 38472097 DOI: 10.1002/jcc.27340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Solvent plays an essential role in a variety of chemical, physical, and biological processes that occur in the solution phase. The reference interaction site model (RISM) and its three-dimensional extension (3D-RISM) serve as powerful computational tools for modeling solvation effects in chemical reactions, biological functions, and structure formations. We present the RISM integrated calculator (RISMiCal) program package, which is based on RISM and 3D-RISM theories with fast GPU code. RISMiCal has been developed as an integrated RISM/3D-RISM program that has interfaces with external programs such as Gaussian16, GAMESS, and Tinker. Fast 3D-RISM programs for single- and multi-GPU codes written in CUDA would enhance the availability of these hybrid methods because they require the performance of many computationally expensive 3D-RISM calculations. We expect that our package can be widely applied for chemical and biological processes in solvent. The RISMiCal package is available at https://rismical-dev.github.io.
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Affiliation(s)
- Yutaka Maruyama
- Data Science Center for Creative Design and Manufacturing, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
- Department of Physics, School of Science and Technology, Meiji University, Kawasaki-shi, Kanagawa, Japan
| | - Norio Yoshida
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Japan
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2
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Colla T, Telles IM, Arfan M, Dos Santos AP, Levin Y. Spiers Memorial Lecture: Towards understanding of iontronic systems: electroosmotic flow of monovalent and divalent electrolyte through charged cylindrical nanopores. Faraday Discuss 2023; 246:11-46. [PMID: 37395363 DOI: 10.1039/d3fd00062a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In many practical applications, ions are the primary charge carrier and must move through either semipermeable membranes or through pores, which mimic ion channels in biological systems. In analogy to electronic devices, the "iontronic" ones use electric fields to induce the charge motion. However, unlike the electrons that move through a conductor, motion of ions is usually associated with simultaneous solvent flow. A study of electroosmotic flow through narrow pores is an outstanding challenge that lies at the interface of non-equilibrium statistical mechanics and fluid dynamics. In this paper, we will review recent works that use dissipative particle dynamics simulations to tackle this difficult problem. We will also present a classical density functional theory (DFT) based on the hypernetted-chain approximation (HNC), which allows us to calculate the velocity of electroosmotic flows inside nanopores containing 1 : 1 or 2 : 1 electrolyte solution. The theoretical results will be compared with simulations. In simulations, the electrostatic interactions are treated using the recently introduced pseudo-1D Ewald summation method. The zeta potentials calculated from the location of the shear plane of a pure solvent are found to agree reasonably well with the Smoluchowski equation. However, the quantitative structure of the fluid velocity profiles deviates significantly from the predictions of the Smoluchowski equation in the case of charged pores with 2 : 1 electrolyte. For low to moderate surface charge densities, the DFT allows us to accurately calculate the electrostatic potential profiles and the zeta potentials inside the nanopores. For pores with 1 : 1 electrolyte, the agreement between theory and simulation is particularly good for large ions, for which steric effects dominate over the ionic electrostatic correlations. The electroosmotic flow is found to depend very strongly on the ionic radii. In the case of pores containing 2 : 1 electrolyte, we observe a reentrant transition in which the electroosmotic flow first reverses and then returns to normal as the surface change density of the pore is increased.
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Affiliation(s)
- Thiago Colla
- Instituto de Física, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
| | - Igor M Telles
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, Porto Alegre, RS, CEP 91501-970, Brazil.
| | - Muhammad Arfan
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, Porto Alegre, RS, CEP 91501-970, Brazil.
| | - Alexandre P Dos Santos
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, Porto Alegre, RS, CEP 91501-970, Brazil.
| | - Yan Levin
- Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, Porto Alegre, RS, CEP 91501-970, Brazil.
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3
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Kournopoulos S, Haslam AJ, Jackson G, Galindo A, Schoen M. Molecular theory of the static dielectric constant of dipolar fluids. J Chem Phys 2022; 156:154111. [PMID: 35459323 DOI: 10.1063/5.0079511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The link between the static dielectric constant and the microscopic intermolecular interactions is the Kirkwood g1 factor, which depends on the orientational structure of the fluid. Over the years, there have been several attempts to provide an accurate description of the orientational structure of dipolar fluids using molecular theories. However, these approaches were either limited to mean-field approximations for the pair correlation function or, more recently, limited to adjusting the orientational dependence to simulation data. Here, we derive a theory for the dielectric constant of dipolar hard-sphere fluids using the augmented modified mean-field approximation. Qualitative agreement is achieved throughout all relevant thermodynamic states, as demonstrated by a comparison with simulation data from the literature. Excellent quantitative agreement can be obtained using a single empirical scaling factor, the physical origin of which is analyzed and accounted for. In order to predict the dielectric constant of the Stockmayer fluid (Lennard-Jones plus dipole potential), we use an adjusted version of the expression for the dipolar hard-sphere fluid. Comparing theoretical predictions with newly generated simulation data, we show that it is possible to obtain excellent agreement with simulation by performing the calculations at a corresponding state using the same scaling factor. Finally, we compare the theoretical orientational structure of the Stockmayer fluid with that obtained from simulations. The simulated structure is calculated following a post-processing methodology that we introduce by deriving an original expression that relates the proposed theory to the histogram of relative dipole angles.
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Affiliation(s)
- S Kournopoulos
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - A J Haslam
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - G Jackson
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - A Galindo
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - M Schoen
- Department of Chemical Engineering, Centre for Process Systems Engineering and Institute for Molecular Science and Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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4
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Bolle J, Bierwirth SP, Požar M, Perera A, Paulus M, Münzner P, Albers C, Dogan S, Elbers M, Sakrowski R, Surmeier G, Böhmer R, Tolan M, Sternemann C. Isomeric effects in structure formation and dielectric dynamics of different octanols. Phys Chem Chem Phys 2021; 23:24211-24221. [PMID: 34693949 DOI: 10.1039/d1cp02468j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The understanding of the microstructure of associated liquids promoted by hydrogen-bonding and constrained by steric hindrance is highly relevant in chemistry, physics, biology and for many aspects of daily life. In this study we use a combination of X-ray diffraction, dielectric spectroscopy and molecular dynamics simulations to reveal temperature induced changes in the microstructure of different octanol isomers, i.e., linear 1-octanol and branched 2-, 3- and 4-octanol. In all octanols, the hydroxyl groups form the basis of chain-, cyclic- or loop-like bonded structures that are separated by outwardly directed alkyl chains. This clustering is analyzed through the scattering pre-peaks observed from X-ray scattering and simulations. The charge ordering which pilots OH aggregation can be linked to the strength of the Debye process observed in dielectric spectroscopy. Interestingly, all methods used here converge to the same interpretation: as one moves from 1-octanol to the branched octanols, the cluster structure evolves from loose large aggregates to a larger number of smaller, tighter aggregates. All alcohols exhibit a peculiar temperature dependence of both the pre-peak and Debye process, which can be understood as a change in microstructure promoted by chain association with increased chain length possibly assisted by ring-opening effects. All these results tend to support the intuitive picture of the entropic constraint provided by branching through the alkyl tails and highlight its capital entropic role in supramolecular assembly.
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Affiliation(s)
- Jennifer Bolle
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - S Peter Bierwirth
- Fakultät Physik, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Martina Požar
- University of Split, Faculty of Science, Ruera Boškovića 33, 21000, Split, Croatia
| | - Aurélien Perera
- Sorbonne Université, Laboratoire de Physique Théorique de la Matiére Condensée (UMR CNRS 7600), 4 Place Jussieu, F75252, Paris cedex 05, France
| | - Michael Paulus
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Philipp Münzner
- Fakultät Physik, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Christian Albers
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Susanne Dogan
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Mirko Elbers
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Robin Sakrowski
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Göran Surmeier
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Roland Böhmer
- Fakultät Physik, Technische Universität Dortmund, 44227 Dortmund, Germany
| | - Metin Tolan
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
| | - Christian Sternemann
- Fakultät Physik/DELTA, Technische Universität Dortmund, 44227 Dortmund, Germany.
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5
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Kalyuzhnyi Y, Patsahan T, Holovko M, Cummings P. Solution of the associative MSA for the patchy colloidal model with dipole-dipole interaction. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Mandal BK, Mishra P. Density functional theory of fluid-solid phase transition in a two-dimensional system of superparamagnetic colloids in tilted magnetic field. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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7
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Pousaneh F, de Wijn AS. Kinetic Theory and Shear Viscosity of Dense Dipolar Hard Sphere Liquids. PHYSICAL REVIEW LETTERS 2020; 124:218004. [PMID: 32530688 DOI: 10.1103/physrevlett.124.218004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Transport properties of dense fluids are fundamentally challenging, because the powerful approaches of equilibrium statistical physics cannot be applied. Polar fluids compound this problem, because the long-range interactions preclude the use of a simple effective diameter approach based solely on hard spheres. Here, we develop a kinetic theory for dipolar hard-sphere fluids that is valid up to high density. We derive a mathematical approximation for the radial distribution function at contact directly from the equation of state, and use it to obtain the shear viscosity. We also perform molecular-dynamics simulations of this system and extract the shear viscosity numerically. The theoretical results compare favorably to the simulations.
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Affiliation(s)
- Faezeh Pousaneh
- Department of Mechanical and Industrial Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Astrid S de Wijn
- Department of Mechanical and Industrial Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
- Department of Physics, Stockholm University, SE-106 91 Stockholm, Sweden
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8
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Rupprecht N, Vural DC. Depletion force between disordered linear macromolecules. Phys Rev E 2020; 101:022607. [PMID: 32168718 DOI: 10.1103/physreve.101.022607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/29/2020] [Indexed: 06/10/2023]
Abstract
When two macromolecules come very near in a fluid, the surrounding molecules, having finite volume, are less likely to get in between. This leads to a pressure difference manifesting as an entropic attraction, called depletion force. Here we calculate the density profile of liquid molecules surrounding a disordered rigid macromolecules modeled as a random arrangement of hard spheres on a linear backbone. We analytically determine the position dependence of the depletion force between two such disordered molecules by calculating the free energy of the system. We then use molecular dynamics simulations to obtain the depletion force between stiff disordered polymers as well as flexible ones and compare the two against each other. We also show how the disorder averaging can be handled starting from the inhomogenous reference interaction site model equations.
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Affiliation(s)
- Nathaniel Rupprecht
- Department of Physics, University of Notre Dame, South Bend, Indiana 46556, USA
| | - Dervis Can Vural
- Department of Physics, University of Notre Dame, South Bend, Indiana 46556, USA
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9
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Jeanmairet G, Rotenberg B, Levesque M, Borgis D, Salanne M. A molecular density functional theory approach to electron transfer reactions. Chem Sci 2018; 10:2130-2143. [PMID: 30881637 PMCID: PMC6385486 DOI: 10.1039/c8sc04512g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/11/2018] [Indexed: 11/21/2022] Open
Abstract
Beyond the dielectric continuum description initiated by Marcus theory, the standard theoretical approach to study electron transfer (ET) reactions in solution or at interfaces is to use classical force field or ab initio molecular dynamics simulations. We present here an alternative method based on liquid-state theory, namely molecular density functional theory, which is numerically much more efficient than simulations while still retaining the molecular nature of the solvent. We begin by reformulating molecular ET theory in a density functional language and show how to compute the various observables characterizing ET reactions from an ensemble of density functional minimizations. In particular, we define within that formulation the relevant order parameter of the reaction, the so-called vertical energy gap, and determine the Marcus free energy curves of both reactant and product states along that coordinate. Important thermodynamic quantities such as the reaction free energy and the reorganization free energies follow. We assess the validity of the method by studying the model Cl0 → Cl+ and Cl0 → Cl- ET reactions in bulk water for which molecular dynamics results are available. The anionic case is found to violate the standard Marcus theory. Finally, we take advantage of the computational efficiency of the method to study the influence of a solid-solvent interface on the ET, by investigating the evolution of the reorganization free energy of the Cl0 → Cl+ reaction when the atom approaches an atomistically resolved wall.
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Affiliation(s)
- Guillaume Jeanmairet
- Sorbonne Université , CNRS , Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux , PHENIX , F-75005 Paris , France . .,Réseau sur le Stockage Électrochimique de l'Énergie (RS2E) , FR CNRS 3459 , 80039 Amiens Cedex , France
| | - Benjamin Rotenberg
- Sorbonne Université , CNRS , Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux , PHENIX , F-75005 Paris , France . .,Réseau sur le Stockage Électrochimique de l'Énergie (RS2E) , FR CNRS 3459 , 80039 Amiens Cedex , France
| | - Maximilien Levesque
- PASTEUR , Département de chimie , École Normale Supérieure , PSL University , Sorbonne Université , CNRS , 75005 Paris , France
| | - Daniel Borgis
- PASTEUR , Département de chimie , École Normale Supérieure , PSL University , Sorbonne Université , CNRS , 75005 Paris , France.,Maison de la Simulation , CEA , CNRS , Université Paris-Sud , UVSQ , Université Paris-Saclay , 91191 Gif-sur-Yvette , France
| | - Mathieu Salanne
- Sorbonne Université , CNRS , Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux , PHENIX , F-75005 Paris , France . .,Réseau sur le Stockage Électrochimique de l'Énergie (RS2E) , FR CNRS 3459 , 80039 Amiens Cedex , France.,Maison de la Simulation , CEA , CNRS , Université Paris-Sud , UVSQ , Université Paris-Saclay , 91191 Gif-sur-Yvette , France
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10
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Affiliation(s)
- Bilin Zhuang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
- Department of Materials Science and Engineering, Institute of High Performance Computing, Singapore 138632, Singapore
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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11
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Belloni L. Exact molecular direct, cavity, and bridge functions in water system. J Chem Phys 2018; 147:164121. [PMID: 29096488 DOI: 10.1063/1.5001684] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The exact molecular bridge function of the extended simple point charge model of liquid water at room temperature is extracted from Monte Carlo (MC) simulation data. The projections gμνmnl(r) onto rotational invariants of the highly directional pair distribution function g(r,Ω) are accumulated during simulation performed with N = 512 molecules (cubic box size L ≈ 25 Å). Making intensive use of anisotropic integral equation techniques, the molecular Ornstein-Zernike equation fed with the MC data available at short distances and completed beyond L/2 with the hypernetted chain closure valid at long distances is then inverted in order to derive on the whole r range the direct correlation function cμνmnl(r), the cavity function yμνmnl(r), the negative excess potential of mean force lnyμνmnl(r), and, finally, the holy grail in such liquid state theory, the bridge function bμνmnl(r) projections. For completeness, the short distance domain inside the soft core can be reached, thanks to the use of a specially designed anisotropic finite potential which replaces the true one between a single pair of molecules in the simulation. The final bridge function b(r,Ω) of bulk water presents strong, non-universal directional features and can now serve as a reference for approximated bridge functions or functionals in liquid physics of aqueous solvents and solutions.
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Affiliation(s)
- Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
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12
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Perera A, Lovrinčević B. A comparative study of aqueous DMSO mixtures by computer simulations and integral equation theories. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1483040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Aurélien Perera
- Laboratoire de Physique Théorique de la Matiére Condensée (UMR CNRS 7600), Université Pierre et Marie Curie, Paris, France
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13
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Colla T, Mohanty PS, Nöjd S, Bialik E, Riede A, Schurtenberger P, Likos CN. Self-Assembly of Ionic Microgels Driven by an Alternating Electric Field: Theory, Simulations, and Experiments. ACS NANO 2018; 12:4321-4337. [PMID: 29634232 DOI: 10.1021/acsnano.7b08843] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The structural properties of a system of ionic microgels under the influence of an alternating electric field are investigated both theoretically and experimentally. This combined investigation aims to shed light on the structural transitions that can be induced by changing either the driving frequency or the strength of the applied field, which range from string-like formation along the field to crystal-like structures across the orthogonal plane. In order to highlight the physical mechanisms responsible for the observed particle self-assembly, we develop a coarse-grained description, in which effective interactions among the charged microgels are induced by both equilibrium ionic distributions and their time-averaged hydrodynamic responses to the applied field. These contributions are modeled by the buildup of an effective dipole moment at the microgels backbones, which is partially screened by their ionic double layer. We show that this description is able to capture the structural properties of this system, allowing for very good agreement with the experimental results. The model coarse-graining parameters are indirectly obtained via the measured pair distribution functions and then further assigned with a clear physical interpretation, allowing us to highlight the main physical mechanisms accounting for the observed self-assembly behavior.
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Affiliation(s)
- Thiago Colla
- Instituto de Física , Universidade Federal de Ouro Preto , CEP 35400-000 Ouro Preto , Minas Gerais , Brazil
- Faculty of Physics , University of Vienna , Boltzmanngasse 5 , 1090 Vienna , Austria
| | - Priti S Mohanty
- Division of Physical Chemistry , Lund University , SE-221 00 Lund , Sweden
- School of Chemical Technology , Kalinga Institute of Industrial Technology (KIIT) , Bhubaneswar 751024 , India
| | - Sofi Nöjd
- Division of Physical Chemistry , Lund University , SE-221 00 Lund , Sweden
| | - Erik Bialik
- Division of Physical Chemistry , Lund University , SE-221 00 Lund , Sweden
| | - Aaron Riede
- Division of Physical Chemistry , Lund University , SE-221 00 Lund , Sweden
| | | | - Christos N Likos
- Faculty of Physics , University of Vienna , Boltzmanngasse 5 , 1090 Vienna , Austria
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14
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Heinen M. Calculating particle pair potentials from fluid-state pair correlations: Iterative ornstein-zernike inversion. J Comput Chem 2018; 39:1531-1543. [DOI: 10.1002/jcc.25225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Marco Heinen
- División de Ciencias e Ingenierías, Departamento de Ingeniería Física; University of Guanajuato, Loma del Bosque 103; León 37150 Mexico
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15
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Feldt J, Miranda S, Pratas F, Roma N, Tomás P, Mata RA. Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program. J Chem Phys 2017; 147:244105. [PMID: 29289129 DOI: 10.1063/1.5009820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.
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Affiliation(s)
- Jonas Feldt
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Sebastião Miranda
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Frederico Pratas
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Nuno Roma
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Pedro Tomás
- INESC-ID/IST, Universidade de Lisboa, Rua Alves Redol, 1000-029 Lisboa, Portugal
| | - Ricardo A Mata
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
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16
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Belloni L, Puibasset J. Finite-size corrections in simulation of dipolar fluids. J Chem Phys 2017; 147:224110. [DOI: 10.1063/1.5005912] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Joël Puibasset
- ICMN, UMR 7374, CNRS et Université d’Orléans, 1B Rue de la Férollerie, 45071 Orléans Cedex, France
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17
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Ding L, Levesque M, Borgis D, Belloni L. Efficient molecular density functional theory using generalized spherical harmonics expansions. J Chem Phys 2017; 147:094107. [DOI: 10.1063/1.4994281] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Lu Ding
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École Normale Supérieure, CNRS, Processus d’Activation Sélective par Transfert d’Énergie Uni-Électronique ou Radiatif (PASTEUR), 75005 Paris, France
| | - Daniel Borgis
- Maison de la Simulation, USR 3441 CNRS-CEA-Université Paris-Saclay, 91191 Gif-sur-Yvette, France
- PASTEUR, Département de Chimie, École Normale Supérieure, UPMC Univ. Paris 06, CNRS, PSL Research University, 75005 Paris, France
- Sorbonne Universités, UPMC Univ. Paris 06, École Normale Supérieure, CNRS, Processus d’Activation Sélective par Transfert d’Énergie Uni-Électronique ou Radiatif (PASTEUR), 75005 Paris, France
| | - Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
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18
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Amano KI, Iwaki M, Hashimoto K, Fukami K, Nishi N, Takahashi O, Sakka T. Number Density Distribution of Small Particles around a Large Particle: Structural Analysis of a Colloidal Suspension. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:11063-11070. [PMID: 27683951 DOI: 10.1021/acs.langmuir.6b02628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Some colloidal suspensions contain two types of particles-small and large particles-to improve the lubricating ability, light absorptivity, and so forth. Structural and chemical analyses of such colloidal suspensions are often performed to understand their properties. In a structural analysis study, the observation of the number density distribution of small particles around a large particle (gLS) is difficult because these particles are randomly moving within the colloidal suspension by Brownian motion. We obtain gLS using the data from a line optical tweezer (LOT) that can measure the potential of mean force between two large colloidal particles (ΦLL). We propose a theory that transforms ΦLL into gLS. The transform theory is explained in detail and tested. We demonstrate for the first time that LOT can be used for the structural analysis of a colloidal suspension. LOT combined with the transform theory will facilitate structural analyses of the colloidal suspensions, which is important for both understanding colloidal properties and developing colloidal products.
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Affiliation(s)
- Ken-Ichi Amano
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
| | - Mitsuhiro Iwaki
- Quantitative Biology Center, RIKEN , Suita, Osaka 565-0874, Japan
- Graduate School of Frontier Biosciences, Osaka University , Suita, Osaka 565-0874, Japan
| | - Kota Hashimoto
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
| | - Kazuhiro Fukami
- Department of Materials Science and Engineering, Graduate School of Engineering, Kyoto University , Kyoto 606-8501, Japan
| | - Naoya Nishi
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
| | - Ohgi Takahashi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University , Sendai 981-8558, Japan
| | - Tetsuo Sakka
- Department of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University , Kyoto 615-8510, Japan
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19
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Dyer KM, Perkyns JS, Pettitt BM. Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:414006. [PMID: 27546725 PMCID: PMC5340275 DOI: 10.1088/0953-8984/28/41/414006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We consider the dielectric response of angularly dependent site-site theories for models of aqueous saline solutions. We find that we can use relatively low order approximations of the angularly dependent correlation functions with correct long ranged behavior to obtain good estimates of the dielectric constant for three site water models and simple 1-1 salts. We find that the solution thermodynamics results for this level of theory, as measured by the Kirkwood G integrals and the excess chemical potentials, are in good quantitative agreement with simulation even when the details of the short ranged structure is not as accurately determined. We find that the dielectric constant predictions of both the pure fluid and the salt-water mixtures are similarly predictive, in comparison to both simulation and experiment.
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Affiliation(s)
- Kippi M Dyer
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, UTMB-Galveston, 301 University Boulevard, Galveston, TX 77555-03004, USA
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20
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Solovyova AY, Goldina OA, Ivanov AO, Lebedev AV, Elfimova EA. The initial magnetic susceptibility of polydisperse ferrofluids: A comparison between experiment and theory over a wide range of concentration. J Chem Phys 2016; 145:084909. [DOI: 10.1063/1.4961405] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anna Y. Solovyova
- Institute of Mathematics and Computer Sciences, Ural Federal University, 51 Lenin Avenue, Ekaterinburg 620000, Russia
| | - Olga A. Goldina
- Institute of Mathematics and Computer Sciences, Ural Federal University, 51 Lenin Avenue, Ekaterinburg 620000, Russia
| | - Alexey O. Ivanov
- Institute of Mathematics and Computer Sciences, Ural Federal University, 51 Lenin Avenue, Ekaterinburg 620000, Russia
| | - Aleksandr V. Lebedev
- Institute of Continuous Media Mechanics, UB RAS, 1 Korolyov st., Perm 614013, Russia
| | - Ekaterina A. Elfimova
- Institute of Mathematics and Computer Sciences, Ural Federal University, 51 Lenin Avenue, Ekaterinburg 620000, Russia
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21
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Jeanmairet G, Levy N, Levesque M, Borgis D. Molecular density functional theory of water including density-polarization coupling. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:244005. [PMID: 27116250 DOI: 10.1088/0953-8984/28/24/244005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.
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Affiliation(s)
- Guillaume Jeanmairet
- Max Planck Institute for Solid State Research, Heisenbergstraße 1, Stuttgart 70569, Germany
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22
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Kido K, Kasahara K, Yokogawa D, Sato H. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach. J Chem Phys 2015; 143:014103. [PMID: 26156461 DOI: 10.1063/1.4923007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.
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Affiliation(s)
- Kentaro Kido
- Nuclear Safety Research Center, Japan Atomic Energy Agency, 2-4 Shirane, Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195, Japan
| | - Kento Kasahara
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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23
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Liu M, Besford QA, Mulvaney T, Gray-Weale A. Order and correlation contributions to the entropy of hydrophobic solvation. J Chem Phys 2015; 142:114117. [PMID: 25796241 DOI: 10.1063/1.4908532] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The entropy of hydrophobic solvation has been explained as the result of ordered solvation structures, of hydrogen bonds, of the small size of the water molecule, of dispersion forces, and of solvent density fluctuations. We report a new approach to the calculation of the entropy of hydrophobic solvation, along with tests of and comparisons to several other methods. The methods are assessed in the light of the available thermodynamic and spectroscopic information on the effects of temperature on hydrophobic solvation. Five model hydrophobes in SPC/E water give benchmark solvation entropies via Widom's test-particle insertion method, and other methods and models are tested against these particle-insertion results. Entropies associated with distributions of tetrahedral order, of electric field, and of solvent dipole orientations are examined. We find these contributions are small compared to the benchmark particle-insertion entropy. Competitive with or better than other theories in accuracy, but with no free parameters, is the new estimate of the entropy contributed by correlations between dipole moments. Dipole correlations account for most of the hydrophobic solvation entropy for all models studied and capture the distinctive temperature dependence seen in thermodynamic and spectroscopic experiments. Entropies based on pair and many-body correlations in number density approach the correct magnitudes but fail to describe temperature and size dependences, respectively. Hydrogen-bond definitions and free energies that best reproduce entropies from simulations are reported, but it is difficult to choose one hydrogen bond model that fits a variety of experiments. The use of information theory, scaled-particle theory, and related methods is discussed briefly. Our results provide a test of the Frank-Evans hypothesis that the negative solvation entropy is due to structured water near the solute, complement the spectroscopic detection of that solvation structure by identifying the structural feature responsible for the entropy change, and point to a possible explanation for the observed dependence on length scale. Our key results are that the hydrophobic effect, i.e. the signature, temperature-dependent, solvation entropy of nonpolar molecules in water, is largely due to a dispersion force arising from correlations between rotating permanent dipole moments, that the strength of this force depends on the Kirkwood g-factor, and that the strength of this force may be obtained exactly without simulation.
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Affiliation(s)
- Maoyuan Liu
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | | | - Thomas Mulvaney
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Angus Gray-Weale
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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24
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Yoshida N. Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method. J Chem Phys 2014; 140:214118. [DOI: 10.1063/1.4879795] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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25
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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.
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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
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26
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Abstract
The existence of a ferroelectric fluid phase for systems of 1000-2000 dipolar hard or soft spheres is well established by numerical simulations. Theoretical approaches proposed to determine the stability of such a phase are either in qualitative agreement with the simulation results or disagree with them. Experimental results for systems of molecules or particles with large electric or magnetic dipole moments are also inconclusive. As a contribution to the question of existence and stability of a fluid ferroelectric phase this simulation work considers system sizes of the order of 10 000 particles, thus an order of magnitude larger than those used in previous studies. It shows that although ferroelectricity is not affected by an increase of system size, different spatial arrangements of the dipolar hard spheres in such a phase are possible whose free energies seem to differ only marginally.
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Affiliation(s)
- D Levesque
- Université de Paris-Sud, Laboratoire de Physique Théorique, UMR8627, Bâtiment 210, 91405 Orsay Cedex, France
| | - J-J Weis
- Université de Paris-Sud, Laboratoire de Physique Théorique, UMR8627, Bâtiment 210, 91405 Orsay Cedex, France
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27
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Belloni L, Chikina I. Efficient full Newton–Raphson technique for the solution of molecular integral equations – example of the SPC/E water-like system. Mol Phys 2014. [DOI: 10.1080/00268976.2014.885612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Wei GW. Multiscale Multiphysics and Multidomain Models I: Basic Theory. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013; 12:10.1142/S021963361341006X. [PMID: 25382892 PMCID: PMC4220694 DOI: 10.1142/s021963361341006x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This work extends our earlier two-domain formulation of a differential geometry based multiscale paradigm into a multidomain theory, which endows us the ability to simultaneously accommodate multiphysical descriptions of aqueous chemical, physical and biological systems, such as fuel cells, solar cells, nanofluidics, ion channels, viruses, RNA polymerases, molecular motors and large macromolecular complexes. The essential idea is to make use of the differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain of solvent from the microscopic domain of solute, and dynamically couple continuum and discrete descriptions. Our main strategy is to construct energy functionals to put on an equal footing of multiphysics, including polar (i.e., electrostatic) solvation, nonpolar solvation, chemical potential, quantum mechanics, fluid mechanics, molecular mechanics, coarse grained dynamics and elastic dynamics. The variational principle is applied to the energy functionals to derive desirable governing equations, such as multidomain Laplace-Beltrami (LB) equations for macromolecular morphologies, multidomain Poisson-Boltzmann (PB) equation or Poisson equation for electrostatic potential, generalized Nernst-Planck (NP) equations for the dynamics of charged solvent species, generalized Navier-Stokes (NS) equation for fluid dynamics, generalized Newton's equations for molecular dynamics (MD) or coarse-grained dynamics and equation of motion for elastic dynamics. Unlike the classical PB equation, our PB equation is an integral-differential equation due to solvent-solute interactions. To illustrate the proposed formalism, we have explicitly constructed three models, a multidomain solvation model, a multidomain charge transport model and a multidomain chemo-electro-fluid-MD-elastic model. Each solute domain is equipped with distinct surface tension, pressure, dielectric function, and charge density distribution. In addition to long-range Coulombic interactions, various non-electrostatic solvent-solute interactions are considered in the present modeling. We demonstrate the consistency between the non-equilibrium charge transport model and the equilibrium solvation model by showing the systematical reduction of the former to the latter at equilibrium. This paper also offers a brief review of the field.
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Affiliation(s)
- Guo-Wei Wei
- Department of Mathematics Michigan State University, MI 48824, USA Department of Electrical and Computer Engineering Michigan State University, MI 48824, USA Department of Biochemistry and Molecular Biology Michigan State University, MI 48824, USA
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29
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Jeanmairet G, Levesque M, Borgis D. Molecular density functional theory of water describing hydrophobicity at short and long length scales. J Chem Phys 2013; 139:154101. [DOI: 10.1063/1.4824737] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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30
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Heinen M, Allahyarov E, Löwen H. Highly asymmetric electrolytes in the primitive model: Hypernetted chain solution in arbitrary spatial dimensions. J Comput Chem 2013; 35:275-89. [DOI: 10.1002/jcc.23446] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 09/03/2013] [Accepted: 09/09/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Marco Heinen
- Institut für Theoretische Physik II; Weiche Materie, Heinrich-Heine-Universität, Düsseldorf, 40225; Düsseldorf Germany
| | - Elshad Allahyarov
- Institut für Theoretische Physik II; Weiche Materie, Heinrich-Heine-Universität, Düsseldorf, 40225; Düsseldorf Germany
- Theoretical Department; Joint Institute for High Temperatures, Russian Academy of Sciences (IVTAN); 13/19 Izhorskaya street Moscow 125412 Russia
| | - Hartmut Löwen
- Institut für Theoretische Physik II; Weiche Materie, Heinrich-Heine-Universität, Düsseldorf, 40225; Düsseldorf Germany
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31
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Ishizuka R, Yoshida N. Extended molecular Ornstein-Zernike integral equation for fully anisotropic solute molecules: Formulation in a rectangular coordinate system. J Chem Phys 2013; 139:084119. [DOI: 10.1063/1.4819211] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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32
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Zhao S, Liu H, Ramirez R, Borgis D. Accurate evaluation of the angular-dependent direct correlation function of water. J Chem Phys 2013; 139:034503. [DOI: 10.1063/1.4813400] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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33
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Jeanmairet G, Levesque M, Vuilleumier R, Borgis D. Molecular Density Functional Theory of Water. J Phys Chem Lett 2013; 4:619-624. [PMID: 26281876 DOI: 10.1021/jz301956b] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three-dimensional implementations of liquid-state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical) molecular density functional theory (MDFT) of water that is derived from first principles and is based on two classical density fields, a scalar one, the particle density, and a vectorial one, the multipolar polarization density. Its implementation requires as input the partial charge distribution of a water molecule and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric constants. It has to be complemented by a solute-solvent three-body term that reinforces tetrahedral order at short-range. The approach is shown to provide the correct 3-D microscopic solvation profile around various molecular solutes, possibly possessing H-bonding sites, at a computer cost two to three orders of magnitude lower than with explicit simulations.
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Affiliation(s)
- Guillaume Jeanmairet
- †Pôle de Physico-Chimie Théorique, École Normale Supérieure, UMR 8640 CNRS-ENS-UPMC, 24, rue Lhomond, 75005 Paris, France
| | - Maximilien Levesque
- †Pôle de Physico-Chimie Théorique, École Normale Supérieure, UMR 8640 CNRS-ENS-UPMC, 24, rue Lhomond, 75005 Paris, France
- ‡Université Pierre et Marie Curie, UMR 7195 PECSA, CNRS-UPMC-ESPCI, 75005 Paris, France
| | - Rodolphe Vuilleumier
- †Pôle de Physico-Chimie Théorique, École Normale Supérieure, UMR 8640 CNRS-ENS-UPMC, 24, rue Lhomond, 75005 Paris, France
| | - Daniel Borgis
- †Pôle de Physico-Chimie Théorique, École Normale Supérieure, UMR 8640 CNRS-ENS-UPMC, 24, rue Lhomond, 75005 Paris, France
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34
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Ingrosso F, Ladanyi BM. Intermolecular Structure and Collective Dynamics of Supercritical Fluoroform Studied by Molecular Dynamics Simulations. J Phys Chem B 2013; 117:654-67. [DOI: 10.1021/jp310246v] [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]
Affiliation(s)
- Francesca Ingrosso
- Theoretical Chemistry and Biochemistry
Group SRSMC UMR 7565, CNRS − Université de Lorraine, Boulevard des Aiguillettes, BP 70239 54506
Vandoeuvre-lès-Nancy Cedex, France
- CNRS, SRSMC, UMR 7565,
Vandoeuvre-lès-Nancy, F-54506, France
| | - Branka M. Ladanyi
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523,
United States
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35
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Kežić B, Perera A. Aqueous tert-butanol mixtures: a model for molecular-emulsions. J Chem Phys 2012; 137:014501. [PMID: 22779659 DOI: 10.1063/1.4730524] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By analogy with micro-emulsion, we introduce the molecular-emulsion picture to describe particular aqueous mixtures. The analogy is set by introducing the equivalent of the Teubner-Strey structure factor, the latter which is traditionally used to describe the structure of micro-emulsions. The main difference resides in the fact that the size of the oil and water domains are not in the micrometer, but in the nanometer scale. This implies that the molecular size and the molecular geometry cannot be neglected anymore. The introduction of this analogy is used to settle the problem of properly describing with computer simulations highly micro-heterogeneous aqueous mixtures. In particular, the issue of whether or not the Kirkwood-Buff integrals represent solely concentration fluctuations is settled by showing the contribution of the micro-heterogeneity to these integrals through the presence of an associated pre-peak in the structure factors. Both the Optimized Potentials for Liquid State (OPLS) and Transferable Potential for Phase Equilibria-United Atoms (TraPPE-UA) force fields for tert-butanol turn out to be remarkably good in describing the structure of the corresponding aqueous mixtures, when the above-mentioned analogy with micro-emulsion is introduced to correct for the computational artifacts in the Kirkwood-Buff integrals.
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Affiliation(s)
- Bernarda Kežić
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600), Université Pierre et Marie Curie, 4 Place Jussieu, F75252 Paris cedex 05, France
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36
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Hagy MC, Hernandez R. Dynamical simulation of dipolar Janus colloids: Equilibrium structure and thermodynamics. J Chem Phys 2012; 137:044505. [DOI: 10.1063/1.4737432] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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37
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Levesque M, Vuilleumier R, Borgis D. Scalar fundamental measure theory for hard spheres in three dimensions: Application to hydrophobic solvation. J Chem Phys 2012; 137:034115. [DOI: 10.1063/1.4734009] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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38
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39
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Puibasset J, Belloni L. Bridge function for the dipolar fluid from simulation. J Chem Phys 2012; 136:154503. [DOI: 10.1063/1.4703899] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Ishizuka R, Yoshida N. Application of efficient algorithm for solving six-dimensional molecular Ornstein-Zernike equation. J Chem Phys 2012; 136:114106. [DOI: 10.1063/1.3693623] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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41
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Borgis D, Gendre L, Ramirez R. Molecular Density Functional Theory: Application to Solvation and Electron-Transfer Thermodynamics in Polar Solvents. J Phys Chem B 2012; 116:2504-12. [DOI: 10.1021/jp210817s] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel Borgis
- Laboratoire PASTEUR, UMR 8640
CNRS-ENS-UPMC, Ecole Normale Supérieure, 24 rue Lhomond, 75231 Paris, France
| | - Lionel Gendre
- Laboratoire LAMBE, CNRS-UMR
8587, Université Evry-Val-d’Essonne, Bd François Mitterand, 91025 Evry, France
| | - Rosa Ramirez
- Laboratoire LAMBE, CNRS-UMR
8587, Université Evry-Val-d’Essonne, Bd François Mitterand, 91025 Evry, France
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42
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Wei GW, Zheng Q, Chen Z, Xia K. Variational multiscale models for charge transport. SIAM REVIEW. SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS 2012; 54:699-754. [PMID: 23172978 PMCID: PMC3501390 DOI: 10.1137/110845690] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
This work presents a few variational multiscale models for charge transport in complex physical, chemical and biological systems and engineering devices, such as fuel cells, solar cells, battery cells, nanofluidics, transistors and ion channels. An essential ingredient of the present models, introduced in an earlier paper (Bulletin of Mathematical Biology, 72, 1562-1622, 2010), is the use of differential geometry theory of surfaces as a natural means to geometrically separate the macroscopic domain from the microscopic domain, meanwhile, dynamically couple discrete and continuum descriptions. Our main strategy is to construct the total energy functional of a charge transport system to encompass the polar and nonpolar free energies of solvation, and chemical potential related energy. By using the Euler-Lagrange variation, coupled Laplace-Beltrami and Poisson-Nernst-Planck (LB-PNP) equations are derived. The solution of the LB-PNP equations leads to the minimization of the total free energy, and explicit profiles of electrostatic potential and densities of charge species. To further reduce the computational complexity, the Boltzmann distribution obtained from the Poisson-Boltzmann (PB) equation is utilized to represent the densities of certain charge species so as to avoid the computationally expensive solution of some Nernst-Planck (NP) equations. Consequently, the coupled Laplace-Beltrami and Poisson-Boltzmann-Nernst-Planck (LB-PBNP) equations are proposed for charge transport in heterogeneous systems. A major emphasis of the present formulation is the consistency between equilibrium LB-PB theory and non-equilibrium LB-PNP theory at equilibrium. Another major emphasis is the capability of the reduced LB-PBNP model to fully recover the prediction of the LB-PNP model at non-equilibrium settings. To account for the fluid impact on the charge transport, we derive coupled Laplace-Beltrami, Poisson-Nernst-Planck and Navier-Stokes equations from the variational principle for chemo-electro-fluid systems. A number of computational algorithms is developed to implement the proposed new variational multiscale models in an efficient manner. A set of ten protein molecules and a realistic ion channel, Gramicidin A, are employed to confirm the consistency and verify the capability. Extensive numerical experiment is designed to validate the proposed variational multiscale models. A good quantitative agreement between our model prediction and the experimental measurement of current-voltage curves is observed for the Gramicidin A channel transport. This paper also provides a brief review of the field.
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Affiliation(s)
- Guo-Wei Wei
- Department of Mathematics Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering Michigan State University, MI 48824, USA
- Address correspondences to Guo-Wei Wei.
| | - Qiong Zheng
- Department of Mathematics Michigan State University, MI 48824, USA
| | - Zhan Chen
- Department of Mathematics Michigan State University, MI 48824, USA
| | - Kelin Xia
- Department of Mathematics Michigan State University, MI 48824, USA
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Chen Z, Baker NA, Wei GW. Differential geometry based solvation model II: Lagrangian formulation. J Math Biol 2011; 63:1139-200. [PMID: 21279359 PMCID: PMC3113640 DOI: 10.1007/s00285-011-0402-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 12/24/2010] [Indexed: 10/18/2022]
Abstract
Solvation is an elementary process in nature and is of paramount importance to more sophisticated chemical, biological and biomolecular processes. The understanding of solvation is an essential prerequisite for the quantitative description and analysis of biomolecular systems. This work presents a Lagrangian formulation of our differential geometry based solvation models. The Lagrangian representation of biomolecular surfaces has a few utilities/advantages. First, it provides an essential basis for biomolecular visualization, surface electrostatic potential map and visual perception of biomolecules. Additionally, it is consistent with the conventional setting of implicit solvent theories and thus, many existing theoretical algorithms and computational software packages can be directly employed. Finally, the Lagrangian representation does not need to resort to artificially enlarged van der Waals radii as often required by the Eulerian representation in solvation analysis. The main goal of the present work is to analyze the connection, similarity and difference between the Eulerian and Lagrangian formalisms of the solvation model. Such analysis is important to the understanding of the differential geometry based solvation model. The present model extends the scaled particle theory of nonpolar solvation model with a solvent-solute interaction potential. The nonpolar solvation model is completed with a Poisson-Boltzmann (PB) theory based polar solvation model. The differential geometry theory of surfaces is employed to provide a natural description of solvent-solute interfaces. The optimization of the total free energy functional, which encompasses the polar and nonpolar contributions, leads to coupled potential driven geometric flow and PB equations. Due to the development of singularities and nonsmooth manifolds in the Lagrangian representation, the resulting potential-driven geometric flow equation is embedded into the Eulerian representation for the purpose of computation, thanks to the equivalence of the Laplace-Beltrami operator in the two representations. The coupled partial differential equations (PDEs) are solved with an iterative procedure to reach a steady state, which delivers desired solvent-solute interface and electrostatic potential for problems of interest. These quantities are utilized to evaluate the solvation free energies and protein-protein binding affinities. A number of computational methods and algorithms are described for the interconversion of Lagrangian and Eulerian representations, and for the solution of the coupled PDE system. The proposed approaches have been extensively validated. We also verify that the mean curvature flow indeed gives rise to the minimal molecular surface and the proposed variational procedure indeed offers minimal total free energy. Solvation analysis and applications are considered for a set of 17 small compounds and a set of 23 proteins. The salt effect on protein-protein binding affinity is investigated with two protein complexes by using the present model. Numerical results are compared to the experimental measurements and to those obtained by using other theoretical methods in the literature.
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Affiliation(s)
- Zhan Chen
- Department of Mathematics, Michigan State University, MI 48824, USA
| | - Nathan A. Baker
- Pacific Northwest National Laboratory,
902 Battelle Boulevard P.O. Box 999, MSIN K7-28, Richland, WA 99352 USA
| | - G. W. Wei
- Department of Mathematics, Michigan State University, MI 48824, USA
- Department of Electrical and Computer Engineering, Michigan State University, MI 48824, USA
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Luo L, Klapp SHL, Chen X. String formation and demixing in monolayers of dipolar colloidal mixtures. J Chem Phys 2011; 135:134701. [DOI: 10.1063/1.3643324] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Howard JJ, Pettitt BM. Integral equations in the study of polar and ionic interaction site fluids. JOURNAL OF STATISTICAL PHYSICS 2011; 145:441-466. [PMID: 22383857 PMCID: PMC3286808 DOI: 10.1007/s10955-011-0260-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this review article we consider some of the current integral equation approaches and application to model polar liquid mixtures. We consider the use of multidimensional integral equations and in particular progress on the theory and applications of three dimensional integral equations. The IEs we consider may be derived from equilibrium statistical mechanical expressions incorporating a classical Hamiltonian description of the system. We give example including salt solutions, inhomogeneous solutions and systems including proteins and nucleic acids.
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Affiliation(s)
- Jesse J Howard
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003
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Wedberg R, O’Connell JP, Peters GH, Abildskov J. Pair correlation function integrals: Computation and use. J Chem Phys 2011; 135:084113. [DOI: 10.1063/1.3626799] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Zhao S, Ramirez R, Vuilleumier R, Borgis D. Molecular density functional theory of solvation: From polar solvents to water. J Chem Phys 2011; 134:194102. [DOI: 10.1063/1.3589142] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Oshima H, Yasuda S, Yoshidome T, Ikeguchi M, Kinoshita M. Crucial importance of the water-entropy effect in predicting hot spots in protein–protein complexes. Phys Chem Chem Phys 2011; 13:16236-46. [DOI: 10.1039/c1cp21597c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Howard JJ, Lynch GC, Pettitt BM. Ion and solvent density distributions around canonical B-DNA from integral equations. J Phys Chem B 2010; 115:547-56. [PMID: 21190358 DOI: 10.1021/jp107383s] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We calculate the water and ion spatial distributions around charged oligonucleotides using a renormalized three-dimensional reference interaction site theory coupled with the HNC closure. Our goal is to understand the balance between inter-DNA strand forces and solvation forces as a function of oligonucleotide length in the short strand limit. The DNA is considered in aqueous electrolyte solutions of 1 M KCl, 0.1 M KCl, or 0.1 M NaCl. The current theoretical results are compared to molecular dynamics (MD) simulations and experiments. It is found that the integral equation (IE) theory replicates the MD and the experimental results for the base-specific hydration patterns in both the major and the minor grooves. We are also able to discern characteristic structural pattern differences between Na(+) and K(+) ions. When compared to Poisson-Boltzmann methods, the IE theory, like simulation, predicts a richly structured ion environment, which is better described as multilayer rather than double layer.
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Affiliation(s)
- Jesse J Howard
- Department of Chemistry, University of Houston, Houston, Texas 77204-5003, USA
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