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Hubman A, Urbic T. Structure and thermodynamics of a 2D Lennard-Jones hexagonal fluid. MOLECULAR SIMULATION 2022; 48:1435-1444. [PMID: 37727614 PMCID: PMC10508885 DOI: 10.1080/08927022.2022.2096219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 06/20/2022] [Indexed: 10/17/2022]
Abstract
The thermodynamic and structural properties of the 2D hexagonal soft-sites fluid are examined by integral equation theory benchmarked against extensive Monte Carlo simulations. Hexamers are built of six equal Lennard-Jones segments. Site-site integral equation theory is used to compute site-site correlation functions, excess internal energies and isotherms over a wide range of conditions and compared with results obtained from Monte Carlo simulations. Various approaches for computing the pressure are discussed as well. Satisfactory qualitative agreement between theory and simulations is found with details depending on the applied closure relation.
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Affiliation(s)
- Anže Hubman
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Tomaz Urbic
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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2
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Lucco Castello F, Tolias P. Bridge functions of classical one-component plasmas. Phys Rev E 2022; 105:015208. [PMID: 35193199 DOI: 10.1103/physreve.105.015208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
In a recent paper, Lucco Castello et al. [arXiv:2107.03537] performed systematic extractions of classical one-component plasma bridge functions from molecular dynamics simulations and provided an accurate parametrization that was incorporated in their isomorph-based empirically modified hypernetted chain approach for Yukawa one-component plasmas. Here the extraction technique and parametrization strategy are described in detail, while the deficiencies of earlier efforts are discussed. The structural and thermodynamic predictions of the updated version of the integral equation theory approach are compared with extensive available simulation results revealing a truly unprecedented level of accuracy in the entire dense liquid region of the Yukawa phase diagram.
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Affiliation(s)
- F Lucco Castello
- Space and Plasma Physics, Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - P Tolias
- Space and Plasma Physics, Royal Institute of Technology, Stockholm SE-100 44, Sweden
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3
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Lucco Castello F, Tolias P, Dyre JC. Testing the isomorph invariance of the bridge functions of Yukawa one-component plasmas. J Chem Phys 2021; 154:034501. [PMID: 33499616 DOI: 10.1063/5.0036226] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been recently conjectured that bridge functions remain nearly invariant along phase diagram lines of constant excess entropy for the broad class of R-simple liquids. To test this hypothesis, the bridge functions of Yukawa systems are computed outside the correlation void with the Ornstein-Zernike inversion method employing structural input from ultra-accurate molecular dynamics simulations and inside the correlation void with the cavity distribution method employing structural input from ultra-long specially designed molecular dynamics simulations featuring a tagged particle pair. Yukawa bridge functions are revealed to be isomorph invariant to a very high degree. The observed invariance is not exact, however, since isomorphic deviations exceed the overall uncertainties.
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Affiliation(s)
- F Lucco Castello
- Space and Plasma Physics, Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - P Tolias
- Space and Plasma Physics, Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - J C Dyre
- Glass and Time, IMFUFA, Roskilde University, Roskilde DK-4000, Denmark
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4
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Kjellander R. A multiple decay-length extension of the Debye-Hückel theory: to achieve high accuracy also for concentrated solutions and explain under-screening in dilute symmetric electrolytes. Phys Chem Chem Phys 2020; 22:23952-23985. [PMID: 33073810 DOI: 10.1039/d0cp02742a] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Poisson-Boltzmann and Debye-Hückel approximations for the pair distributions and mean electrostatic potential in electrolytes predict that these entities have one single decay mode with a decay length equal to the Debye length 1/κD, that is, they have a characteristic contribution that decays with distance r like e-κDr/r. However, in reality, electrolytes have several decay modes e-κr/r, e-κ'r/r etc. with different decay lengths, 1/κ, 1/κ' etc., that in general are different from the Debye length. As an illustration of the significance of multiple decay modes in electrolytes, the present work uses a very simple extension of the Debye-Hückel approximation with two decay lengths, which predicts oscillatory modes when appropriate. This approach gives very accurate results for radial distribution functions and thermodynamic properties of aqueous solutions of monovalent electrolytes for all concentrations investigated, including high ones. It is designed to satisfy necessary statistical mechanical conditions for the distributions. The effective dielectric permittivity of the electrolyte plays an important role in the theory and each mode has its own value of this entity. Electrolytes with high electrostatic coupling, like those with multivalent ions and/or with solvent of low dielectric constant, have decay lengths in dilute solutions that substantially deviate from the Debye length. It is shown that this is caused by nonlinear ion-ion correlation effects and the origin of under-screening, i.e., 1/κ > 1/κD, in dilute symmetric electrolytes is analyzed. The under-screening is accompanied by an increase in the effective dielectric permittivity that is also caused by these correlations. The theoretical results for the decay length are successfully compared with recent experimental data for simple electrolytes in various solvents. The paper includes background material on electrolyte theory and screening in order to be accessible for nonexperts in the field.
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Affiliation(s)
- Roland Kjellander
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden.
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5
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Mkanya A, Pellicane G, Ramos FS, Ramos AM, Lee LL. On the structure, property, and phase behaviour of the symmetric Yukawa mixtures: testing of the consistent integral equation theories. Mol Phys 2019. [DOI: 10.1080/00268976.2018.1542165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Anele Mkanya
- School of Chemistry and Physics, University of Kwazulu-Natal, Pietermaritzburg, South Africa
- National Institute for Theoretical Physics (NITheP), KZN node, Pietermaritzburg, South Africa
| | - Giuseppe Pellicane
- School of Chemistry and Physics, University of Kwazulu-Natal, Pietermaritzburg, South Africa
- National Institute for Theoretical Physics (NITheP), KZN node, Pietermaritzburg, South Africa
| | - Franklin S. Ramos
- Department of Chemical and Materials Engineering, California State University, Pomona, CA, USA
| | - Ana M. Ramos
- Department of Chemical and Materials Engineering, California State University, Pomona, CA, USA
| | - Lloyd L. Lee
- School of Chemistry and Physics, University of Kwazulu-Natal, Pietermaritzburg, South Africa
- Department of Chemical and Materials Engineering, California State University, Pomona, CA, USA
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6
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Amano KI, Hayashi T, Hashimoto K, Nishi N, Sakka T. Potential of mean force between spherical particles in an ionic liquid and its decomposition into energetic and entropic components: An analysis using an integral equation theory. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.02.089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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7
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8
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Vyalov I, Chuev G, Georgi N. Solute-solvent cavity and bridge functions. I. Varying size of the solute. J Chem Phys 2014; 141:074505. [PMID: 25149799 DOI: 10.1063/1.4892876] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- I Vyalov
- Max-Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - G Chuev
- Max-Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
| | - N Georgi
- Max-Planck Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig 04103, Germany
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9
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Xu M, Zhang C, Du Z, Mi J. Structures and Surface Tensions of Fluids near Solid Surfaces: An Integral Equation Theory Study. J Phys Chem B 2012; 116:6514-21. [DOI: 10.1021/jp301991k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Mengjin Xu
- The Key Laboratory of Carbon
Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing
100029, Peopleʼs Republic of China
| | - Chen Zhang
- The Key Laboratory of Carbon
Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing
100029, Peopleʼs Republic of China
| | - Zhongjie Du
- The Key Laboratory of Carbon
Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing
100029, Peopleʼs Republic of China
| | - Jianguo Mi
- State Key Laboratory of Organic−Inorganic
Composites, Beijing University of Chemical Technology, Beijing 100029, China
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10
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Lee LL. Constructing a new closure theory based on the third-order Ornstein-Zernike equation and a study of the adsorption of simple fluids. J Chem Phys 2011; 135:204706. [DOI: 10.1063/1.3663221] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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11
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A star-function based density functional study of the adsorption of Lennard-Jones fluid near its supercritical states. J Supercrit Fluids 2010. [DOI: 10.1016/j.supflu.2010.09.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Zhou S, Solana JR. Inquiry into thermodynamic behavior of hard sphere plus repulsive barrier of finite height. J Chem Phys 2009; 131:204503. [PMID: 19947690 DOI: 10.1063/1.3265984] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shiqi Zhou
- State Key Laboratory of Powder Metallurgy, Central South University, Changsha, Hunan 410083, China.
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13
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Verma A, Ford DM. Closure-based perturbative density-functional theory of hard-sphere freezing: properties of the bridge functional. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:031109. [PMID: 19905064 DOI: 10.1103/physreve.80.031109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Indexed: 05/28/2023]
Abstract
The study of freezing using perturbative classical density-functional theory is revisited, using a bridge functional approach to resum all terms beyond second order in the free energy expansion. More precisely, the first-order direct correlation function of the solid phase is written as a functional expansion about the homogeneous liquid phase, and the sum of all higher-order terms is represented as a functional of the second-order term. Information about the shape and uniqueness of this bridge functional for the case of hard spheres is obtained via an inversion procedure that employs Monte Carlo fluid-solid coexistence data from the literature. The parametric plots obtained from the inversion procedure show very little scatter in certain regions, suggesting a unique functional dependence, but large scatter in other regions. The scatter is related to the anisotropy of the solid lattice at the particle scale. Interestingly, the thermodynamic properties of the phase transition are quite insensitive to the regions where the scatter is large, and several simple closures (i.e., analytical forms of the bridge function) reproduce exactly the liquid-solid coexistence densities and Lindemann parameter from simulation. The form of these closures is significantly different from the usual closures employed in liquid-state integral equation theory.
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Affiliation(s)
- Anurag Verma
- Department of Chemical Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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14
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Chung TH, Lee LL. The mean activity coefficients of 2:2 electrolyte solutions: An integral equation study of the restricted primitive model. J Chem Phys 2009; 130:134513. [DOI: 10.1063/1.3099335] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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15
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Cheung DL, Anton L, Allen MP, Masters AJ, Phillips J, Schmidt M. Structure and stability of isotropic states of hard platelet fluids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:041201. [PMID: 18999406 DOI: 10.1103/physreve.78.041201] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Indexed: 05/27/2023]
Abstract
We study the thermodynamics and the pair structure of hard, infinitely thin, circular platelets in the isotropic phase. Monte Carlo simulation results indicate a rich spatial structure of the spherical expansion components of the direct correlation function, including nonmonotonical variation of some of the components with density. Integral equation theory is shown to reproduce the main features observed in simulations. The hypernetted chain closure, as well as its extended versions that include the bridge function up to second and third order in density, perform better than both the Percus-Yevick closure and Verlet bridge function approximation. Using a recent fundamental measure density functional theory, an analytic expression for the direct correlation function is obtained as the sum of the Mayer bond and a term proportional to the density and the intersection length of two platelets. This is shown to give a reasonable estimate of the structure found in simulations, but to fail to capture the nonmonotonic variation with density. We also carry out a density functional stability analysis of the isotropic phase with respect to nematic ordering and show that the limiting density is consistent with that where the Kerr coefficient vanishes. As a reference system, we compare to simulation results for hard oblate spheroids with small, but nonzero elongations, demonstrating that the case of vanishingly thin platelets is approached smoothly.
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Affiliation(s)
- David L Cheung
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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16
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Freedman H, Le L, Tuszynski JA, Truong TN. Improving the Performance of the Coupled Reference Interaction Site Model−Hyper-netted Chain (RISM−HNC)/Simulation Method for Free Energy of Solvation. J Phys Chem B 2008; 112:2340-8. [DOI: 10.1021/jp077179l] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Holly Freedman
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
| | - Ly Le
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
| | - Jack A. Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
| | - Thanh N. Truong
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, AB, Canada, AB T6G 1Z2, Department of Physics, University of Alberta, 11322-89 Avenue, Edmonton, AB, Canada, AB T6G 2G7, and Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112
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17
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Cheung DL, Anton L, Allen MP, Masters AJ. Structure of molecular liquids: hard rod-disk mixtures. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:011202. [PMID: 18351843 DOI: 10.1103/physreve.77.011202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Indexed: 05/26/2023]
Abstract
The structure of hard rod-disk mixtures is studied using Monte Carlo simulations and integral equation theory, for a range of densities in the isotropic phase. By extension of methods used in single component fluids, the pair correlation functions of the molecules are calculated and comparisons between simulation and integral equation theory, using a number of different closure relations, are made. Comparison is also made for thermodynamic data and phase behavior.
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Affiliation(s)
- David L Cheung
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom
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18
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Cheung DL, Anton L, Allen MP, Masters AJ. Structure of molecular liquids: closure relations for hard spheroids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:041201. [PMID: 17994971 DOI: 10.1103/physreve.76.041201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Indexed: 05/25/2023]
Abstract
We present the results of Monte Carlo simulations of hard spheroids of revolution of different elongations. Both prolate and oblate shapes are examined. A systematic study of the bridge function b(1,2), and direct comparison with the indirect correlation function gamma(1,2)=h(1,2)-c(1,2) at densities spanning the isotropic fluid range, allow us to evaluate the accuracy of various proposed closure relations for integral equations.
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Affiliation(s)
- David L Cheung
- Department of Physics and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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19
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Zhang L, Jinno M, Davis HT, White HS. Molecular Dynamics and Hypernetted Chain Equation Studies of Soft Core Repulsions in Electrolyte Solutions. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927029408022532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Lianrui Zhang
- a Department of Chemical Engineering and Materials Science , University of Minnesota , Minneapolis , MN , 55455
| | - M. Jinno
- a Department of Chemical Engineering and Materials Science , University of Minnesota , Minneapolis , MN , 55455
- b Mitsubishi Heavy Industries, Ltd. , 10 Oye-cho, Minatoku , Nagoya , 455 , Japan
| | - H. Ted Davis
- a Department of Chemical Engineering and Materials Science , University of Minnesota , Minneapolis , MN , 55455
| | - Henry S. White
- a Department of Chemical Engineering and Materials Science , University of Minnesota , Minneapolis , MN , 55455
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20
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Affiliation(s)
- Bedamati Das
- a Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur , 208016 , India
| | - Pinaki Gupta-Bhaya
- a Department of Chemistry , Indian Institute of Technology Kanpur , Kanpur , 208016 , India
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21
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Wilson DS, Lee LL. Chemical potentials and phase equilibria of Lennard-Jones mixtures: a self-consistent integral equation approach. J Chem Phys 2005; 123:044512. [PMID: 16095374 DOI: 10.1063/1.1961399] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We explore the vapor-liquid phase behavior of binary mixtures of Lennard-Jones-type molecules where one component is supercritical, given the system temperature. We apply the self-consistency approach to the Ornstein-Zernike integral equations to obtain the correlation functions. The consistency checks include not only thermodynamic consistencies (pressure consistency and Gibbs-Duhem consistency), but also pointwise consistencies, such as the zero-separation theorems on the cavity functions. The consistencies are enforced via the bridge functions in the closure which contain adjustable parameters. The full solution requires the values of not only the monomer chemical potentials, but also the dimer chemical potentials present in the zero-separation theorems. These are evaluated by the direct chemical-potential formula [L. L. Lee, J. Chem. Phys. 97, 8606 (1992)] that does not require temperature nor density integration. In order to assess the integral equation accuracy, molecular-dynamics simulations are carried out alongside the states studied. The integral equation results compare well with simulation data. In phase calculations, it is important to have pressure consistency and valid chemical potentials, since the matching of phase boundaries requires the equality of the pressures and chemical potentials of both the liquid and vapor phases. The mixtures studied are methane-type and pentane-type molecules, both characterized by effective Lennard-Jones potentials. Calculations on one isotherm show that the integral equation approach yields valid answers as compared with the experimental data of Sage and Lacey. To study vapor-liquid phase behavior, it is necessary to use consistent theories; any inconsistencies, especially in pressure, will vitiate the phase boundary calculations.
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Affiliation(s)
- D Scott Wilson
- School of Chemical, Biological, and Materials Engineering, University of Oklahoma, Norman, Oklahoma 73072, USA
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22
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Freedman H, Truong TN. A Coupled Reference Interaction Site Model/Molecular Dynamics Study of the Potential of Mean Force Curve of the SN2 Cl- + CH3Cl Reaction in Water. J Phys Chem B 2005; 109:4726-30. [PMID: 16851554 DOI: 10.1021/jp044944c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An application of the coupled reference interaction site model (RISM)/simulation methodology to the calculation of the potential of mean force (PMF) curve in aqueous solution for the identity nucleophilic substitution reaction Cl(-) + CH(3)Cl is performed. The free energy of activation is calculated to be 27.1 kcal/mol which compares very well with the experimentally determined barrier height of 26.6 kcal/mol. Furthermore, the calculated PMF is almost superimposed with that previously calculated using the computationally rigorous Monte Carlo with importance sampling method (Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154). Using the calculated PMF, a crude estimate of the solvated kinetic transmission coefficient also compares well with that of previous more accurate simulations. These results indicate that the coupled RISM/simulation method provides a cost-effective methodology for studying reactions in solution.
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Affiliation(s)
- Holly Freedman
- Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Freedman H, Nguyen HN, Truong TN. A Study of the Tautomeric Equilibria of 2-Hydroxypyridine/2-Oxopyridine and of Cytosine in Water Using the Coupled Reference Interaction Site Model(RISM)/Molecular Dynamics (MD) Approach. J Phys Chem B 2004. [DOI: 10.1021/jp046453y] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Holly Freedman
- Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, room 2020, Salt Lake City, Utah 84112-0850
| | - Hung N. Nguyen
- Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, room 2020, Salt Lake City, Utah 84112-0850
| | - Thanh N. Truong
- Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, 315 South 1400 East, room 2020, Salt Lake City, Utah 84112-0850
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24
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Freedman H, Truong TN. Coupled reference interaction site model/simulation approach for thermochemistry of solvation: Theory and prospects. J Chem Phys 2004; 121:2187-98. [PMID: 15260773 DOI: 10.1063/1.1760741] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a new methodology for computing solvation free energy, which is based upon the reference interaction site model (RISM)/hypernetted chain (HNC) solvation free energy expression, but which substitutes radial distribution functions taken from simulations for those calculated by simultaneous solution of the RISM and HNC equations. Consequently, solvation free energy can be obtained from a single molecular dynamics or Monte Carlo simulation. Here we describe in detail the coupled RISM/simulation approach, and offer some error analysis. Finally we give the results of its application to a set of small test molecules in aqueous solution. The success shown in some of our results demonstrates that the coupled RISM/simulation approach is worth considering further as a potentially useful tool in studies of solvated systems, such as aqueous molecular biosystems.
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Affiliation(s)
- Holly Freedman
- Department of Chemistry, Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City 84112, USA
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25
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Fantoni R, Pastore G. Computer simulation study of the closure relations in hard sphere fluids. J Chem Phys 2004; 120:10681-90. [PMID: 15268094 DOI: 10.1063/1.1739392] [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
We study, using Monte Carlo simulations, the cavity and the bridge functions of various hard sphere fluids: one component system, equimolar additive, and nonadditive binary mixtures. In particular, we numerically check the assumption of local dependency of the bridge functions from the indirect correlation functions, on which most of the existing integral equation theories hinge. We find that this condition can be violated either in the region around the first and second neighbors shell, or inside the hard core, for the systems here considered. The violations manifest themselves clearly in the so-called Duh-Haymet plots of the bridge functions versus the indirect correlation functions and become amplified as the coupling of the system increases.
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Affiliation(s)
- R Fantoni
- Dipartimento di Fisica Teorica dell' Università and Istituto Nazionale di Fisica della Materia, Strada Costiera 11, 34014 Trieste, Italy.
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26
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Freedman H, Truong TN. An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide. J Chem Phys 2004; 121:12447-56. [PMID: 15606265 DOI: 10.1063/1.1818046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an application of our recently proposed coupled reference interaction site model (RISM) molecular dynamics (MD) solvation free energy methodology [Freedman and Truong, Chem. Phys. Lett. 381, 362 (2003); J. Chem. Phys. 121, 2187 (2004)] to study the conformational stability of alanine dipeptide in aqueous solution. In this methodology, radial distribution functions obtained from a single MD simulation are substituted into a RISM expression for solvation free energy. Consequently, iterative solution of the RISM equation is not needed. The relative solvation free energies of seven different conformations of the alanine dipeptide in aqueous solution are calculated. Results from the coupled RISM/MD methodology are in good agreement with those from earlier simulations using the accurate free energy perturbation approach, showing that the alphaR conformation is most stabilized by solution. This study establishes a framework for applying this coupled RISM/MD method to larger biological systems.
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Affiliation(s)
- Holly Freedman
- Henry Eyring Center for Theoretical Chemistry, Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Dyer K, Perkyns J, Pettitt BM. Computationally useful bridge diagram series. III. Lennard-Jones mixtures. J Chem Phys 2002. [DOI: 10.1063/1.1473661] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
28
|
Perkyns JS, Dyer KM, Pettitt BM. Computationally useful bridge diagram series. II. Diagrams inh-bonds. J Chem Phys 2002. [DOI: 10.1063/1.1473660] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
29
|
BOOTH MICHAELJ, HAYMET ADJ. Molten salts near a charged surface: integral equation approximation for a model of KCl. Mol Phys 2001. [DOI: 10.1080/00268970110075167] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
30
|
Kinoshita M, Imai T, Kovalenko A, Hirata F. Improvement of the reference interaction site model theory for calculating the partial molar volume of amino acids and polypeptides. Chem Phys Lett 2001. [DOI: 10.1016/s0009-2614(01)01129-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
31
|
Taşseven Ç, Enrique González L, Silbert M, Alcaraz O, Trullàs J. The bridge functions of molten salts. J Chem Phys 2001. [DOI: 10.1063/1.1392366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
32
|
Eaton AC, Haymet ADJ. Electrolytes at charged interfaces: Pair integral equation approximations for model 2–2 electrolytes. J Chem Phys 2001. [DOI: 10.1063/1.1375141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
33
|
Lee LL, Malijevsky A. Structures and properties of hard sphere mixtures based on a self-consistent integral equation. J Chem Phys 2001. [DOI: 10.1063/1.1359182] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
34
|
Hribar B, Vlachy V, Trokhymchuk A, Pizio O. Structure and Thermodynamics of Asymmetric Electrolytes Adsorbed in Disordered Electroneutral Charged Matrices from Replica Ornstein−Zernike Equations. J Phys Chem B 1999. [DOI: 10.1021/jp990253i] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
35
|
|
36
|
Ulander J, Kjellander R. Screening and asymptotic decay of pair distributions in asymmetric electrolytes. J Chem Phys 1998. [DOI: 10.1063/1.477613] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
37
|
Weis JJ, Levesque D, Caillol JM. Restricted primitive model of an ionic solution confined to a plane. J Chem Phys 1998. [DOI: 10.1063/1.477371] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
38
|
KJELLANDER ROLAND, ULANDER JOHAN. Effective ionic charges, permittivity and screening length: dressed ion theory applied to 1:2 electrolyte solutions. Mol Phys 1998. [DOI: 10.1080/00268979809483184] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
39
|
Hribar B, Pizio O, Trokhymchuk A, Vlachy V. Ion–ion correlations in electrolyte solutions adsorbed in disordered electroneutral charged matrices from replica Ornstein–Zernike equations. J Chem Phys 1998. [DOI: 10.1063/1.476819] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
40
|
Lee LL. The potential distribution-based closures to the integral equations for liquid structure: The Lennard-Jones fluid. J Chem Phys 1997. [DOI: 10.1063/1.474974] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
41
|
Anta JA, Lomba E, Alvarez M, Martı́n C, Lombardero M. Integral equation approaches to mixtures of atomic and molecular fluids. J Chem Phys 1997. [DOI: 10.1063/1.473372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
42
|
Kinoshita M, Iba S, Harada M. Interaction between macroparticles in aqueous electrolytes. J Chem Phys 1996. [DOI: 10.1063/1.472037] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
43
|
Lee LL, Ghonasgi D, Lomba E. The fluid structures for soft‐sphere potentials via the zero‐separation theorems on molecular distribution functions. J Chem Phys 1996. [DOI: 10.1063/1.471522] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
44
|
Duh D, Henderson D. Integral equation theory for Lennard‐Jones fluids: The bridge function and applications to pure fluids and mixtures. J Chem Phys 1996. [DOI: 10.1063/1.471391] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
45
|
Das B, Gupta-Bhaya P. Hypernetted chain calculation of static correlation function of macroions in solution using Allnatt equation. Mol Phys 1995. [DOI: 10.1080/00268979500102821] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
46
|
|
47
|
Lee LL. An accurate integral equation theory for hard spheres: Role of the zero‐separation theorems in the closure relation. J Chem Phys 1995. [DOI: 10.1063/1.469998] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
48
|
|
49
|
Duh D, Haymet ADJ. Integral equation theory for uncharged liquids: The Lennard‐Jones fluid and the bridge function. J Chem Phys 1995. [DOI: 10.1063/1.470724] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
50
|
Booth MJ, Eaton AC, Haymet ADJ. Electrolytes at charged interfaces: Integral equation theory for 2–2 and 1–1 model electrolytes. J Chem Phys 1995. [DOI: 10.1063/1.469608] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|