1
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Wilding NB, Evans R, Turci F. What is the best simulation approach for measuring local density fluctuations near solvo-/hydrophobes? J Chem Phys 2024; 160:164103. [PMID: 38651807 DOI: 10.1063/5.0203088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Measurements of local density fluctuations are crucial to characterizing the interfacial properties of equilibrium fluids. A specific case that has been well-explored involves the heightened compressibility of water near hydrophobic entities. Commonly, a spatial profile of local fluctuation strength is constructed from the measurements of the mean and variance of solvent particle number fluctuations in a set of contiguous subvolumes of the system adjacent to the solvo-/hydrophobe. An alternative measure proposed by Evans and Stewart [J. Phys.: Condens. Matter 27, 194111 (2015)] defines a local compressibility profile in terms of the chemical potential derivative of the spatial number density profile. Using Grand canonical Monte Carlo simulation, we compare and contrast the efficacy of these two approaches for a Lennard-Jones solvent at spherical and planar solvophobic interfaces and SPC/E water at a hydrophobic spherical solute. Our principal findings are as follows: (i) the local compressibility profile χ(r) of Evans and Stewart is considerably more sensitive to variations in the strength of local density fluctuations than the spatial fluctuation profile F(r) and can resolve much more detailed structure; and (ii) while the local compressibility profile is essentially independent of the choice of spatial discretization used to construct the profile, the spatial fluctuation profile exhibits a strong systematic dependence on the size of the subvolumes on which the profile is defined. We clarify the origin and nature of this finite-size effect.
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Affiliation(s)
- Nigel B Wilding
- H.H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Robert Evans
- H.H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Francesco Turci
- H.H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
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2
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Paterson T, Bannerman MN, Lue L. Using the Zeno line to assess and refine molecular models. J Chem Phys 2024; 160:154503. [PMID: 38624125 DOI: 10.1063/5.0192770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 04/01/2024] [Indexed: 04/17/2024] Open
Abstract
The Zeno line is the locus of points on the temperature-density plane where the compressibility factor of the fluid is equal to one. It has been observed to be straight for a broad variety of real fluids, although the underlying reasons for this are still unclear. In this work, a detailed study of the Zeno line and its relation to the vapor-liquid coexistence curve is performed for two simple model pair-potential fluids: attractive square-well fluids with varying well-widths λ and Mie n-6 fluids with different repulsive exponents n. Interestingly, the Zeno lines of these fluids are curved, regardless of the value of λ or n. We find that for square-well fluids, λ ≈ 1.8 presents a Zeno line, which is the most linear over the largest temperature range. For Mie n-6 fluids, we find that the straightest Zeno line occurs for n between 8 and 10. Additionally, the square-well and Mie fluids with the straightest Zeno line showed the closest quantitative agreement with the vapor-liquid coexistence curve for experimental fluids that follow the principle of corresponding states (e.g., argon, xenon, krypton, methane, nitrogen, and oxygen). These results suggest that the Zeno line can provide a useful additional feature, in complement to other properties, such as the phase envelope, to evaluate molecular models.
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Affiliation(s)
- Thomas Paterson
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
| | - Marcus N Bannerman
- School of Engineering, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Leo Lue
- Department of Chemical and Process Engineering, University of Strathclyde, James Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United Kingdom
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3
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Höfling F, Dietrich S. Structure of liquid-vapor interfaces: Perspectives from liquid state theory, large-scale simulations, and potential grazing-incidence x-ray diffraction. J Chem Phys 2024; 160:104107. [PMID: 38469908 DOI: 10.1063/5.0186955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
Grazing-incidence x-ray diffraction (GIXRD) is a scattering technique that allows one to characterize the structure of fluid interfaces down to the molecular scale, including the measurement of surface tension and interface roughness. However, the corresponding standard data analysis at nonzero wave numbers has been criticized as to be inconclusive because the scattering intensity is polluted by the unavoidable scattering from the bulk. Here, we overcome this ambiguity by proposing a physically consistent model of the bulk contribution based on a minimal set of assumptions of experimental relevance. To this end, we derive an explicit integral expression for the background scattering, which can be determined numerically from the static structure factors of the coexisting bulk phases as independent input. Concerning the interpretation of GIXRD data inferred from computer simulations, we extend the model to account also for the finite sizes of the bulk phases, which are unavoidable in simulations. The corresponding leading-order correction beyond the dominant contribution to the scattered intensity is revealed by asymptotic analysis, which is characterized by the competition between the linear system size and the x-ray penetration depth in the case of simulations. Specifically, we have calculated the expected GIXRD intensity for scattering at the planar liquid-vapor interface of Lennard-Jones fluids with truncated pair interactions via extensive, high-precision computer simulations. The reported data cover interfacial and bulk properties of fluid states along the whole liquid-vapor coexistence line. A sensitivity analysis shows that our findings are robust with respect to the detailed definition of the mean interface position. We conclude that previous claims of an enhanced surface tension at mesoscopic scales are amenable to unambiguous tests via scattering experiments.
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Affiliation(s)
- F Höfling
- Freie Universität Berlin, Fachbereich Mathematik und Informatik, Arnimallee 6, 14195 Berlin, Germany
- Zuse Institut Berlin, Takustr. 7, 14195 Berlin, Germany
| | - S Dietrich
- Max-Planck-Institut für Intelligente Systeme, Heisenbergstraße 3, 70569 Stuttgart, Germany
- IV. Institut für Theoretische Physik, Universität Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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4
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An R, Addington CK, Long Y, Rotnicki K, Śliwinska-Bartkowiak M, Thommes M, Gubbins KE. The Nanoscale Wetting Parameter and Its Role in Interfacial Phenomena: Phase Transitions in Nanopores. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:18730-18745. [PMID: 38095601 DOI: 10.1021/acs.langmuir.3c01925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Through analysis of the statistical mechanical equations for a thin adsorbed film (gas, liquid, or solid) on a solid substrate or confined within a pore, it is possible to express the equilibrium thermodynamic properties of the film as a function of just two dimensionless parameters: a nanoscale wetting parameter, αw, and pore width, H*. The wetting parameter, αw, is defined in terms of molecular parameters for the adsorbed film and substrate and so is applicable at the nanoscale and for films of any phase. The main assumptions in the treatment are that (a) the substrate structure is not significantly affected by the adsorbed layer and (b) the diameter of the adsorbate molecules is not very small compared to the spacing of atoms in the solid substrate. We show that different surface geometries of the substrate (e.g., slit, cylindrical, and spherical pores) and various models of wall heterogeneity can be accounted for through a well-defined correction to the wetting parameter; no new dimensionless variables are introduced. Experimental measurements are reported for contact angles for various liquids on several planar substrates and are shown to be closely correlated with the nanoscale wetting parameter. We apply this approach to phase separation in nanopores of various geometries. Molecular simulation results for the phase diagram in confinement, obtained by the flat histogram Monte Carlo method, are reported and are shown to be closely similar to experimental results for capillary condensation, melting, and the triple point. The value of the wetting parameter, αw, is shown to determine the qualitative behavior (e.g., increase vs decrease in the melting temperature, capillary condensation vs evaporation), whereas the pore width determines the magnitude of the confinement effect. The triple point temperature and pressure for the confined phase are always lower than those for the bulk phase for all cases studied.
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Affiliation(s)
- Rong An
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners' Way, Raleigh, North Carolina 27695-7905, United States
- School of Materials Science and Engineering/Herbert Gleiter Institute of Nanoscience, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Cody K Addington
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners' Way, Raleigh, North Carolina 27695-7905, United States
- U.S. E.P.A., Center for Computational Toxicology & Exposure, Office of Research & Development, Research Triangle Park, North Carolina 27711, United States
| | - Yun Long
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners' Way, Raleigh, North Carolina 27695-7905, United States
- College of Computing, Georgia Institute of Technology, 801 Atlantic Drive, Atlanta, Georgia 30318, United States
| | - Konrad Rotnicki
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, Poznan 61-614, Poland
| | | | - Matthias Thommes
- Department of Chemical & Bioengineering, Friedrich-Alexander Universitaet Erlangen-Nurernberg, Erlangen 91058, Germany
| | - Keith E Gubbins
- Department of Chemical & Biomolecular Engineering, North Carolina State University, 911 Partners' Way, Raleigh, North Carolina 27695-7905, United States
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5
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Cho Y, Jacobs WM. Nonequilibrium interfacial properties of chemically driven fluids. J Chem Phys 2023; 159:154101. [PMID: 37843057 DOI: 10.1063/5.0166824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/26/2023] [Indexed: 10/17/2023] Open
Abstract
Chemically driven fluids can demix to form condensed droplets that exhibit phase behaviors not observed at equilibrium. In particular, nonequilibrium interfacial properties can emerge when the chemical reactions are driven differentially between the interior and exterior of the phase-separated droplets. Here, we use a minimal model to study changes in the interfacial tension between coexisting phases away from equilibrium. Simulations of both droplet nucleation and interface roughness indicate that the nonequilibrium interfacial tension can either be increased or decreased relative to its equilibrium value, depending on whether the driven chemical reactions are accelerated or decelerated within the droplets. Finally, we show that these observations can be understood using a predictive theory based on an effective thermodynamic equilibrium.
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Affiliation(s)
- Yongick Cho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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6
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Biswas S, Chung Y, Ramirez J, Wu H, Green WH. Predicting Critical Properties and Acentric Factors of Fluids Using Multitask Machine Learning. J Chem Inf Model 2023; 63:4574-4588. [PMID: 37487557 DOI: 10.1021/acs.jcim.3c00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Knowledge of critical properties, such as critical temperature, pressure, density, as well as acentric factor, is essential to calculate thermo-physical properties of chemical compounds. Experiments to determine critical properties and acentric factors are expensive and time intensive; therefore, we developed a machine learning (ML) model that can predict these molecular properties given the SMILES representation of a chemical species. We explored directed message passing neural network (D-MPNN) and graph attention network as ML architecture choices. Additionally, we investigated featurization with additional atomic and molecular features, multitask training, and pretraining using estimated data to optimize model performance. Our final model utilizes a D-MPNN layer to learn the molecular representation and is supplemented by Abraham parameters. A multitask training scheme was used to train a single model to predict all the critical properties and acentric factors along with boiling point, melting point, enthalpy of vaporization, and enthalpy of fusion. The model was evaluated on both random and scaffold splits where it shows state-of-the-art accuracies. The extensive data set of critical properties and acentric factors contains 1144 chemical compounds and is made available in the public domain together with the source code that can be used for further exploration.
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Affiliation(s)
- Sayandeep Biswas
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yunsie Chung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Josephine Ramirez
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Haoyang Wu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Eckert T, Stuhlmüller NCX, Sammüller F, Schmidt M. Local measures of fluctuations in inhomogeneous liquids: statistical mechanics and illustrative applications. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2023; 35:425102. [PMID: 37414000 DOI: 10.1088/1361-648x/ace50c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 07/08/2023]
Abstract
We show in detail how three one-body fluctuation profiles, namely the local compressibility, the local thermal susceptibility, and the reduced density, can be obtained from a statistical mechanical many-body description of classical particle-based systems. We present several different and equivalent routes to the definition of each fluctuation profile, facilitating their explicit numerical calculation in inhomogeneous equilibrium systems. This underlying framework is used for the derivation of further properties such as hard wall contact theorems and novel types of inhomogeneous one-body Ornstein-Zernike equations. The practical accessibility of all three fluctuation profiles is exemplified by grand canonical Monte Carlo simulations that we present for hard sphere, Gaussian core and Lennard-Jones fluids in confinement.
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Affiliation(s)
- Tobias Eckert
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Nico C X Stuhlmüller
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Florian Sammüller
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
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8
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Abstract
Biomolecular condensates constitute a newly recognized form of spatial organization in living cells. Although many condensates are believed to form as a result of phase separation, the physicochemical properties that determine the phase behavior of heterogeneous biomolecular mixtures are only beginning to be explored. Theory and simulation provide invaluable tools for probing the relationship between molecular determinants, such as protein and RNA sequences, and the emergence of phase-separated condensates in such complex environments. This review covers recent advances in the prediction and computational design of biomolecular mixtures that phase-separate into many coexisting phases. First, we review efforts to understand the phase behavior of mixtures with hundreds or thousands of species using theoretical models and statistical approaches. We then describe progress in developing analytical theories and coarse-grained simulation models to predict multiphase condensates with the molecular detail required to make contact with biophysical experiments. We conclude by summarizing the challenges ahead for modeling the inhomogeneous spatial organization of biomolecular mixtures in living cells.
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Affiliation(s)
- William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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9
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Pruteanu CG, Bannerman MN, Kirsz M, Lue L, Ackland GJ. From Atoms to Colloids: Does the Frenkel Line Exist in Discontinuous Potentials? ACS OMEGA 2023; 8:12144-12153. [PMID: 37033816 PMCID: PMC10077443 DOI: 10.1021/acsomega.2c08056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
The Frenkel line has been proposed as a crossover in the fluid region of phase diagrams between a "nonrigid" and a "rigid" fluid. It is generally described as a crossover in the dynamical properties of a material and as such has been described theoretically using a very different set of markers from those with which is it investigated experimentally. In this study, we have performed extensive calculations using two simple yet fundamentally different model systems: hard spheres and square-well potentials. The former has only hardcore repulsion, while the latter also includes a simple model of attraction. We computed and analyzed a series of physical properties used previously in simulations and experimental measurements and discuss critically their correlations and validity as to being able to uniquely and coherently locate the Frenkel line in discontinuous potentials.
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Affiliation(s)
- Ciprian G. Pruteanu
- SUPA,
School of Physics and Astronomy and Centre for Science at Extreme
Conditions, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - Marcus N. Bannerman
- School
of Engineering, University of Aberdeen, Aberdeen AB24 3UE, United Kingdom
| | - Marcin Kirsz
- SUPA,
School of Physics and Astronomy and Centre for Science at Extreme
Conditions, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
| | - Leo Lue
- Department
of Chemical and Process Engineering, University
of Strathclyde, James
Weir Building, 75 Montrose Street, Glasgow G1 1XJ, United
Kingdom
| | - Graeme J. Ackland
- SUPA,
School of Physics and Astronomy and Centre for Science at Extreme
Conditions, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom
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10
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Cho Y, Jacobs WM. Tuning Nucleation Kinetics via Nonequilibrium Chemical Reactions. PHYSICAL REVIEW LETTERS 2023; 130:128203. [PMID: 37027881 DOI: 10.1103/physrevlett.130.128203] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/21/2023] [Indexed: 06/19/2023]
Abstract
Unlike fluids at thermal equilibrium, biomolecular mixtures in living systems can sustain nonequilibrium steady states, in which active processes modify the conformational states of the constituent molecules. Despite qualitative similarities between liquid-liquid phase separation in these systems, the extent to which the phase-separation kinetics differ remains unclear. Here we show that inhomogeneous chemical reactions can alter the nucleation kinetics of liquid-liquid phase separation in a manner that is consistent with classical nucleation theory, but can only be rationalized by introducing a nonequilibrium interfacial tension. We identify conditions under which nucleation can be accelerated without changing the energetics or supersaturation, thus breaking the correlation between fast nucleation and strong driving forces that is typical of phase separation and self-assembly at thermal equilibrium.
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Affiliation(s)
- Yongick Cho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - William M Jacobs
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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11
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Krishnamurthy S, Mathews Kalapurakal RA, Mani E. Computer simulations of self-assembly of anisotropic colloids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:273001. [PMID: 35172296 DOI: 10.1088/1361-648x/ac55d6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Computer simulations have played a significant role in understanding the physics of colloidal self-assembly, interpreting experimental observations, and predicting novel mesoscopic and crystalline structures. Recent advances in computer simulations of colloidal self-assembly driven by anisotropic or orientation-dependent inter-particle interactions are highlighted in this review. These interactions are broadly classified into two classes: entropic and enthalpic interactions. They mainly arise due to shape anisotropy, surface heterogeneity, compositional heterogeneity, external field, interfaces, and confinements. Key challenges and opportunities in the field are discussed.
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Affiliation(s)
- Sriram Krishnamurthy
- Polymer Engineering and Colloids Science Laboratory, Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai-600036, India
| | - Remya Ann Mathews Kalapurakal
- Polymer Engineering and Colloids Science Laboratory, Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai-600036, India
| | - Ethayaraja Mani
- Polymer Engineering and Colloids Science Laboratory, Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai-600036, India
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12
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Coe MK, Evans R, Wilding NB. The coexistence curve and surface tension of a monatomic water model. J Chem Phys 2022; 156:154505. [PMID: 35459314 DOI: 10.1063/5.0085252] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the monatomic water model of Molinero and Moore the grand canonical ensemble Monte Carlo simulation. Measurements of the probability distribution of the number density obtained via multicanonical sampling and histogram reweighting provide accurate estimates of the temperature dependence of both the liquid-vapor coexistence densities and the surface tension. Using finite-size scaling methods, we locate the liquid-vapor critical point at Tc = 917.6 K, ρc = 0.311 g cm-3. When plotted in scaled variables, in order to test the law of corresponding states, the coexistence curve of monatomic water is close to that of real water. In this respect, it performs better than extended simple point charge (SPC/E), TIP4P, and TIP4P/2005 water.
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Affiliation(s)
- Mary K Coe
- H.H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Robert Evans
- H.H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Nigel B Wilding
- H.H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
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13
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Siderius DW, Hatch HW, Errington JR, Shen VK. Comments on “Monte Carlo Simulations for Water Adsorption in Porous Materials: Best Practices and New Insights” †. AIChE J 2022. [DOI: 10.1002/aic.17686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel W. Siderius
- Chemical Sciences Division National Institute of Standards and Technology Gaithersburg Maryland USA
| | - Harold W. Hatch
- Chemical Sciences Division National Institute of Standards and Technology Gaithersburg Maryland USA
| | - Jeffrey R. Errington
- Department of Chemical and Biological Engineering University at Buffalo Buffalo New York USA
| | - Vincent K. Shen
- Chemical Sciences Division National Institute of Standards and Technology Gaithersburg Maryland USA
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14
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Coe MK, Evans R, Wilding NB. Density Depletion and Enhanced Fluctuations in Water near Hydrophobic Solutes: Identifying the Underlying Physics. PHYSICAL REVIEW LETTERS 2022; 128:045501. [PMID: 35148161 DOI: 10.1103/physrevlett.128.045501] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
We investigate the origin of the density depletion and enhanced density fluctuations that occur in water in the vicinity of an extended hydrophobic solute. We argue that both phenomena are remnants of the critical drying surface phase transition that occurs at liquid-vapor coexistence in the macroscopic planar limit, i.e., as the solute radius R_{s}→∞. Focusing on the density profile ρ(r) and a sensitive spatial measure of fluctuations, the local compressibility profile χ(r), we develop a scaling theory which expresses the extent of the density depletion and enhancement in compressibility in terms of R_{s}, the strength of solute-water attraction ϵ_{s}, and the deviation from liquid-vapor coexistence δμ. Testing the predictions against results of classical density functional theory for a simple solvent and grand canonical Monte Carlo simulations of a popular water model, we find that the theory provides a firm physical basis for understanding how water behaves at a hydrophobe.
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Affiliation(s)
- Mary K Coe
- H. H. Wills Physics Lab, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - Robert Evans
- H. H. Wills Physics Lab, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
| | - Nigel B Wilding
- H. H. Wills Physics Lab, University of Bristol, Tyndall Avenue, Bristol BS8 1TL, United Kingdom
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15
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Kobayashi H, Rohrbach PB, Scheichl R, Wilding NB, Jack RL. Critical point for demixing of binary hard spheres. Phys Rev E 2021; 104:044603. [PMID: 34781560 DOI: 10.1103/physreve.104.044603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/22/2021] [Indexed: 11/07/2022]
Abstract
We use a two-level simulation method to analyze the critical point associated with demixing of binary hard-sphere mixtures. The method exploits an accurate coarse-grained model with two- and three-body effective interactions. Using this model within the two-level methodology allows computation of properties of the full (fine-grained) mixture. The critical point is located by computing the probability distribution for the number of large particles in the grand canonical ensemble and matching to the universal form for the 3D Ising universality class. The results have a strong and unexpected dependence on the size ratio between large and small particles, which is related to three-body effective interactions and the geometry of the underlying hard-sphere packings.
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Affiliation(s)
- Hideki Kobayashi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Paul B Rohrbach
- DAMTP, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Robert Scheichl
- Institute for Applied Mathematics, Heidelberg University, INF 205, 69120 Heidelberg, Germany.,Department of Mathematical Sciences, University of Bath, Bath BA2 7AY, United Kingdom
| | - Nigel B Wilding
- H. H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Robert L Jack
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.,DAMTP, University of Cambridge, Centre for Mathematical Sciences, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
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16
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Rana U, Brangwynne CP, Panagiotopoulos AZ. Phase separation vs aggregation behavior for model disordered proteins. J Chem Phys 2021; 155:125101. [PMID: 34598580 DOI: 10.1063/5.0060046] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) is widely utilized by the cell to organize and regulate various biochemical processes. Although the LLPS of proteins is known to occur in a sequence-dependent manner, it is unclear how sequence properties dictate the nature of the phase transition and thereby influence condensed phase morphology. In this work, we have utilized grand canonical Monte Carlo simulations for a simple coarse-grained model of disordered proteins to systematically investigate how sequence distribution, sticker fraction, and chain length impact the formation of finite-size aggregates, which can preempt macroscopic phase separation for some sequences. We demonstrate that a normalized sequence charge decoration (SCD) parameter establishes a "soft" predictive criterion for distinguishing when a model protein undergoes macroscopic phase separation vs finite aggregation. Additionally, we find that this order parameter is strongly correlated with the critical density for phase separation, highlighting an unambiguous connection between sequence distribution and condensed phase density. Results obtained from an analysis of the order parameter reveal that at sufficiently long chain lengths, the vast majority of sequences are likely to phase separate. Our results suggest that classical LLPS should be the primary phase transition for disordered proteins when short-ranged attractive interactions dominate and suggest a possible reason behind recent findings of widespread phase separation throughout living cells.
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Affiliation(s)
- Ushnish Rana
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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17
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Escobedo FA. On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration. J Chem Phys 2021; 155:114112. [PMID: 34551542 DOI: 10.1063/5.0061541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points involved. On the one hand, commonly used FEP techniques based on overlap sampling leverage the full information contained in the overlapping macrostate probability distributions. On the other hand, conventional TI methods only use information on the first moments of those distributions, as embodied by the first derivatives of the free energy. Since the accuracy of simulation data degrades considerably for high-order moments (for FEP) or free-energy derivatives (for TI), it is proposed to consider, consistently for both methods, data up to second-order moments/derivatives. This provides a compromise between the limiting strategies embodied by common FEP and TI and leads to simple, optimized expressions to evaluate free-energy differences. The proposed formulas are validated with an analytically solvable harmonic Hamiltonian (for assessing systematic errors), an atomistic system (for computing the potential of mean force with coordinate-dependent order parameters), and a binary-component coarse-grained model (for tracing a solid-liquid phase diagram in an ensemble sampled through alchemical transformations). It is shown that the proposed FEP and TI formulas are straightforward to implement, perform similarly well, and allow robust estimation of free-energy differences even when the spacing of successive points does not guarantee them to have proper overlapping in phase space.
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Affiliation(s)
- Fernando A Escobedo
- Robert Frederick Smith School of Chemistry and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
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18
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Naincy Attri, Sudhir K. Singh. Estimation of Pore Critical Temperature of Nanoconfined Alkanes Using Vapour-Liquid Interfacial Free Energy. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2021. [DOI: 10.1134/s1990793121090037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Li Z, Winisdoerffer C, Soubiran F, Caracas R. Ab initio Gibbs ensemble Monte Carlo simulations of the liquid-vapor equilibrium and the critical point of sodium. Phys Chem Chem Phys 2021; 23:311-319. [PMID: 33347522 DOI: 10.1039/d0cp04158k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The ab initio (ai) Gibbs ensemble (GE) Monte Carlo (MC) method coupled with Kohn-Sham density functional theory is successful in predicting the liquid-vapour equilibrium of insulating systems. Here we show that the aiGEMC method can be used to study also metallic systems, where the excited electronic states play an important role and cannot be neglected. For this we include the electronic free energy in the formulation of the effective energy of the system to be used in the acceptance criteria for the MC moves. The application of this aiGEMC method to sodium yields a good agreement with available experimental data on the liquid-vapour equilibrium densities. We predict a critical point for sodium at 2338 ± 108 K and 0.24 ± 0.03 g cm-3. The liquid structure stemming from aiGEMC simulations is very similar to the one from ab initio molecular dynamics. Since this method can determine phase transition without computing the Gibbs free energy, it may offer a new possibility to study other materials with a reasonable computational cost.
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Affiliation(s)
- Zhi Li
- CNRS, École Normale Supérieure de Lyon, Laboratoire de Géologie de Lyon LGLTPE UMR 5276, 46 allée d'Italie, Lyon 69364, France.
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20
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Sadus RJ. Combining intermolecular potentials for the prediction of fluid properties: Two-body and three-body interactions. J Chem Phys 2020; 153:214509. [DOI: 10.1063/5.0033466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Richard J. Sadus
- Centre for Computational Innovations, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
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21
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Abstract
The role of cohesive r-4 interactions on the existence of a vapor phase and the formation of vapor-liquid equilibria is investigated by performing molecular simulations for the n-4 potential. The cohesive r-4 interactions delay the emergence of a vapor phase until very high temperatures. The critical temperature is up to 5 times higher than normal fluids, as represented by the Lennard-Jones potential. The greatest overall influence on vapor-liquid equilibria is observed for the 5-4 potential, which is the lowest repulsive limit of the potential. Increasing n initially mitigates the influence of r-4 interactions, but the moderating influence declines for n > 12. A relationship is reported between the critical temperature and the Boyle temperature, which allows the critical temperature to be determined for a given n value. The n-4 potential could provide valuable insight into the behavior of non-conventional materials with both very low vapor pressures at elevated temperatures and highly dipolar interactions.
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Affiliation(s)
- Richard J Sadus
- Centre for Computational Innovations, Swinburne University of Technology, P.O. Box 218, Hawthorn, Victoria 3122, Australia
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22
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Wohlfahrt O, Dellago C, Sega M. Ab initio structure and thermodynamics of the RPBE-D3 water/vapor interface by neural-network molecular dynamics. J Chem Phys 2020; 153:144710. [DOI: 10.1063/5.0021852] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Oliver Wohlfahrt
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Christoph Dellago
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Marcello Sega
- University of Vienna, Faculty of Physics, Boltzmanngasse 5, A-1090 Vienna, Austria
- Forschungszentrum Jülich GmbH, Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Fürther Str. 248, D-90429 Nürnberg, Germany
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23
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Gobbo D, Ballone P, Garabato BD. Coarse-Grained Model of Entropy-Driven Demixing. J Phys Chem B 2020; 124:9267-9274. [DOI: 10.1021/acs.jpcb.0c07575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Gobbo
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - P. Ballone
- School of Physics, University College, Dublin 4, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College, Dublin 4, Ireland
| | - B. D. Garabato
- Computational and Chemical Biology, Fondazione Istituto Italiano di Tecnologia, Genova 16163, Italy
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24
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Jung H, Yethiraj A. Phase behavior of continuous-space systems: A supervised machine learning approach. J Chem Phys 2020; 153:064904. [DOI: 10.1063/5.0014194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Hyuntae Jung
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Arun Yethiraj
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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25
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Kulkarni A, García EJ, Damone A, Schappals M, Stephan S, Kohns M, Hasse H. A Force Field for Poly(oxymethylene) Dimethyl Ethers (OME n). J Chem Theory Comput 2020; 16:2517-2528. [PMID: 32227933 DOI: 10.1021/acs.jctc.9b01106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A united atom force field for the homologous series of the poly(oxymethylene) dimethyl ethers (OMEn), H3C-O-(CH2O)n-CH3, is presented. OMEn are oxygenates and promising new synthetic fuels and solvents. The molecular geometry of the OMEn, the internal degrees of freedom, and their electrostatic properties were obtained from quantum mechanical calculations. To model repulsion and dispersion, Lennard-Jones parameters were fitted to the experimental liquid densities and vapor pressures of pure OMEn (n = 1-4). The critical properties of OMEn (n = 1-4) were determined from the simulation data. Additionally, the shear viscosity of pure liquid OMEn is evaluated and compared with literature data. Finally, the solubility of CO2 in OME2, OME3, and OME4 is predicted using a literature model for CO2 and the Lorentz-Berthelot combining rules. The results agree well with experimental data from the literature.
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Affiliation(s)
- Aditya Kulkarni
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
| | - Edder J García
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
| | - Angelo Damone
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
| | - Michael Schappals
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
| | - Simon Stephan
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
| | - Maximilian Kohns
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
| | - Hans Hasse
- Laboratory of Engineering Thermodynamics (LTD), Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 44, 67663 Kaiserslautern, Germany
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26
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Xu J, Ferrenberg AM, Landau DP. High-resolution Monte Carlo study of the order-parameter distribution of the three-dimensional Ising model. Phys Rev E 2020; 101:023315. [PMID: 32168706 DOI: 10.1103/physreve.101.023315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 01/29/2020] [Indexed: 11/07/2022]
Abstract
We apply extensive Monte Carlo simulations to study the probability distribution P(m) of the order parameter m for the simple cubic Ising model with periodic boundary condition at the transition point. Sampling is performed with the Wolff cluster flipping algorithm, and histogram reweighting together with finite-size scaling analyses are then used to extract a precise functional form for the probability distribution of the magnetization, P(m), in the thermodynamic limit. This form should serve as a benchmark for other models in the three-dimensional Ising universality class.
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Affiliation(s)
- Jiahao Xu
- Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA
| | - Alan M Ferrenberg
- Department of Computer Science and Software Engineering, Miami University of Ohio, Oxford, Ohio 45056, USA
| | - David P Landau
- Center for Simulational Physics, University of Georgia, Athens, Georgia 30602, USA
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27
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A unified description of hydrophilic and superhydrophobic surfaces in terms of the wetting and drying transitions of liquids. Proc Natl Acad Sci U S A 2019; 116:23901-23908. [PMID: 31611388 DOI: 10.1073/pnas.1913587116] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clarifying the factors that control the contact angle of a liquid on a solid substrate is a long-standing scientific problem pertinent across physics, chemistry, and materials science. Progress has been hampered by the lack of a comprehensive and unified understanding of the physics of wetting and drying phase transitions. Using various theoretical and simulational techniques applied to realistic fluid models, we elucidate how the character of these transitions depends sensitively on both the range of fluid-fluid and substrate-fluid interactions and the temperature. Our calculations uncover previously unrecognized classes of surface phase diagram which differ from that established for simple lattice models and often assumed to be universal. The differences relate both to the topology of the phase diagram and to the nature of the transitions, with a remarkable feature being a difference between drying and wetting transitions which persists even in the approach to the bulk critical point. Most experimental and simulational studies of liquids at a substrate belong to one of these previously unrecognized classes. We predict that while there appears to be nothing particularly special about water with regard to its wetting and drying behavior, superhydrophobic behavior should be more readily observable in experiments conducted at high temperatures than at room temperature.
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28
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Kobayashi H, Rohrbach PB, Scheichl R, Wilding NB, Jack RL. Correction of coarse-graining errors by a two-level method: Application to the Asakura-Oosawa model. J Chem Phys 2019; 151:144108. [DOI: 10.1063/1.5120833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Hideki Kobayashi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Paul B. Rohrbach
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Robert Scheichl
- Institute for Applied Mathematics, Heidelberg University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Nigel B. Wilding
- H.H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Robert L. Jack
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
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29
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Campos-Villalobos G, Ravipati S, Haslam AJ, Jackson G, Suaste J, Gil-Villegas A. Modelling adsorption using an augmented two-dimensional statistical associating fluid theory: 2D-SAFT-VR Mie. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1665724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Srikanth Ravipati
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
| | - Andrew J. Haslam
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
| | - George Jackson
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK
| | - Jonatan Suaste
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, León, México
| | - Alejandro Gil-Villegas
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, León, México
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30
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Affiliation(s)
- James Losey
- Centre for Computational Innovations, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
| | - Richard J. Sadus
- Centre for Computational Innovations, Swinburne University of Technology, PO Box 218, Hawthorn, Victoria 3122, Australia
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31
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Bianco V, Franzese G. Hydrogen bond correlated percolation in a supercooled water monolayer as a hallmark of the critical region. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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32
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Abstract
The idea that water is a mixture of two distinct states is analyzed in some detail. It is shown that the known compressibility of water is in fact sufficiently small that for a volume of water of size 1 nm3, the density fluctuations are of order 4% of the average density. This is much smaller than the ≈25% density fluctuations that would be required for significant regions of high and low density water to occur on this volume scale. It is also pointed out that the density fluctuations in water are, if anything, smaller than those that occur in other common liquids which do not have the anomalous properties of water. It is shown that if the distribution of density fluctuations is unimodal, the system is in the one-phase region, and if bimodal, it is in the two-phase region. None of the liquid or amorphous phases of water explored in this work give any sign of being in the two-phase region. Existing neutron and X-ray scattering data on water in the amorphous phases, and in the stable liquid phases as a function pressure and temperature, are subject to a new set of empirical potential structure refinement simulations. These simulations are interrogated for their configurational entropy, using a spherical harmonic reconstruction of the full orientational pair correlation function. It is shown that the excess pair entropy derived from this function, plus the known perfect gas contributions, give a reasonable account of the total entropy of water, within the likely errors. This estimated entropy follows the expected declining trend with decreasing temperature. Evidence that higher density water will have higher entropy than lower density water emerges, in accordance with what is expected from the negative thermal expansion coefficient of water at low temperatures. However, this entropy increase is not large and goes through a maximum before declining at yet higher densities and pressures, in a manner reminiscent of what has been previously observed in the diffusion coefficient as a function of pressure. There is no evidence that ambient water can be regarded as patches of high density, high entropy and low density, low entropy liquid, as some have claimed, since high density water has a similar entropy to low density water. There is some evidence that the distinction between these two states will become more pronounced as the temperature is lowered. Extensive discussion of the use of order parameters to describe water structure is given, and it is pointed out that these indices generally cannot be used to infer two-state behavior.
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Affiliation(s)
- A K Soper
- ISIS Facility, UKRI-STFC Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire OX11 0QX, United Kingdom
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33
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Waibel C, Gross J. Polarizable Transferable Anisotropic United-Atom Force Field Based on the Mie Potential for Phase Equilibria: Ethers, n-Alkanes, and Nitrogen. J Chem Theory Comput 2019; 15:2561-2573. [DOI: 10.1021/acs.jctc.8b01238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Christian Waibel
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
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34
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Sadus RJ. Molecular simulation of orthobaric isochoric heat capacities near the critical point. Phys Rev E 2019; 99:012139. [PMID: 30780235 DOI: 10.1103/physreve.99.012139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Indexed: 06/09/2023]
Abstract
A molecular simulation strategy is investigated for detecting the divergence of the isochoric heat capacity (C_{V}) on the vapor and liquid coexistence branches of a fluid near the critical point. The procedure is applied to the empirical Lennard-Jones potential and accurate state-of-the-art ab initio two-body and two-body + three-body potentials for argon. Simulations with the Lennard-Jones potential predict the divergence of C_{V}, and the phenomenon is also observed for both two-body and two-body + three body potentials. The potentials also correctly predict the crossover between vapor and liquid C_{V} values and the subcritical liquid C_{V} minimum, which marks the commencement C_{V} divergence. The effect of three-body interactions is to delay the onset of divergence to higher subcritical temperatures.
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Affiliation(s)
- Richard J Sadus
- Centre for Computational Innovations, Swinburne University of Technology, P.O. Box 218 Hawthorn, Victoria 3122, Australia
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35
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Waibel C, Feinler MS, Gross J. A Modified Shifted Force Approach to the Wolf Summation. J Chem Theory Comput 2018; 15:572-583. [PMID: 30418767 DOI: 10.1021/acs.jctc.8b00343] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Wolf method for calculation of electrostatic interactions in molecular simulations is known to describe the energy well, whereas the forces have discontinuities. For a more reliable description of the forces this method can be extended with a shifted force approach. This leads to a good description of the forces and precise molecular dynamics simulation, but the description of the energy becomes poorer. In this study we propose a modification of a shifted force extension to describe the energy as well as the forces in better agreement to reference data as determined from the Ewald summation. We show that vapor-liquid phase equilibria (VLE) calculated with Monte Carlo simulations in the grand canonical ensemble and dynamic properties calculated with molecular dynamics simulations can be calculated reliably using this modification to describe the electrostatic interactions.
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Affiliation(s)
- Christian Waibel
- Institute of Thermodynamics and Thermal Process Engineering , University of Stuttgart , Pfaffenwaldring 9 , 70569 Stuttgart , Germany
| | - Mathias Simon Feinler
- Institute of Thermodynamics and Thermal Process Engineering , University of Stuttgart , Pfaffenwaldring 9 , 70569 Stuttgart , Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering , University of Stuttgart , Pfaffenwaldring 9 , 70569 Stuttgart , Germany
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36
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Desgranges C, Delhommelle J. A new approach for the prediction of partition functions using machine learning techniques. J Chem Phys 2018; 149:044118. [DOI: 10.1063/1.5037098] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Caroline Desgranges
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, North Dakota 58202, USA
| | - Jerome Delhommelle
- Department of Chemistry, University of North Dakota, 151 Cornell Street Stop 9024, Grand Forks, North Dakota 58202, USA
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37
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Law JO, Wong AG, Kusumaatmaja H, Miller MA. Nucleation on a sphere: the roles of curvature, confinement and ensemble. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1483041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Jack O. Law
- Department of Physics, Durham University, Durham, UK
| | - Alex G. Wong
- Department of Chemistry, Durham University, Durham, UK
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38
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Mahynski NA, Errington JR, Shen VK. Temperature extrapolation of multicomponent grand canonical free energy landscapes. J Chem Phys 2018; 147:054105. [PMID: 28789543 DOI: 10.1063/1.4996759] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We derive a method for extrapolating the grand canonical free energy landscape of a multicomponent fluid system from one temperature to another. Previously, we introduced this statistical mechanical framework for the case where kinetic energy contributions to the classical partition function were neglected for simplicity [N. A. Mahynski et al., J. Chem. Phys. 146, 074101 (2017)]. Here, we generalize the derivation to admit these contributions in order to explicitly illustrate the differences that result. Specifically, we show how factoring out kinetic energy effects a priori, in order to consider only the configurational partition function, leads to simpler mathematical expressions that tend to produce more accurate extrapolations than when these effects are included. We demonstrate this by comparing and contrasting these two approaches for the simple cases of an ideal gas and a non-ideal, square-well fluid.
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Affiliation(s)
- Nathan A Mahynski
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, USA
| | - Jeffrey R Errington
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, USA
| | - Vincent K Shen
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, USA
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39
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Jamali SH, Wolff L, Becker TM, Bardow A, Vlugt TJH, Moultos OA. Finite-Size Effects of Binary Mutual Diffusion Coefficients from Molecular Dynamics. J Chem Theory Comput 2018; 14:2667-2677. [PMID: 29664633 PMCID: PMC5943679 DOI: 10.1021/acs.jctc.8b00170] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics simulations were performed for the prediction of the finite-size effects of Maxwell-Stefan diffusion coefficients of molecular mixtures and a wide variety of binary Lennard-Jones systems. A strong dependency of computed diffusivities on the system size was observed. Computed diffusivities were found to increase with the number of molecules. We propose a correction for the extrapolation of Maxwell-Stefan diffusion coefficients to the thermodynamic limit, based on the study by Yeh and Hummer ( J. Phys. Chem. B , 2004 , 108 , 15873 - 15879 ). The proposed correction is a function of the viscosity of the system, the size of the simulation box, and the thermodynamic factor, which is a measure for the nonideality of the mixture. Verification is carried out for more than 200 distinct binary Lennard-Jones systems, as well as 9 binary systems of methanol, water, ethanol, acetone, methylamine, and carbon tetrachloride. Significant deviations between finite-size Maxwell-Stefan diffusivities and the corresponding diffusivities at the thermodynamic limit were found for mixtures close to demixing. In these cases, the finite-size correction can be even larger than the simulated (finite-size) Maxwell-Stefan diffusivity. Our results show that considering these finite-size effects is crucial and that the suggested correction allows for reliable computations.
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Affiliation(s)
- Seyed Hossein Jamali
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft University of Technology , Leeghwaterstraat 39 , 2628CB Delft , The Netherlands
| | - Ludger Wolff
- Institute of Technical Thermodynamics , RWTH Aachen University , 52056 Aachen , Germany
| | - Tim M Becker
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft University of Technology , Leeghwaterstraat 39 , 2628CB Delft , The Netherlands
| | - André Bardow
- Institute of Technical Thermodynamics , RWTH Aachen University , 52056 Aachen , Germany
| | - Thijs J H Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft University of Technology , Leeghwaterstraat 39 , 2628CB Delft , The Netherlands
| | - Othonas A Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering , Delft University of Technology , Leeghwaterstraat 39 , 2628CB Delft , The Netherlands
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40
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Ogunronbi KE, Sepehri A, Chen B, Wyslouzil BE. Vapor phase nucleation of the short-chain n-alkanes (n-pentane, n-hexane and n-heptane): Experiments and Monte Carlo simulations. J Chem Phys 2018; 148:144312. [DOI: 10.1063/1.5023567] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kehinde E. Ogunronbi
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Aliasghar Sepehri
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, USA
| | - Bin Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, USA
| | - Barbara E. Wyslouzil
- William G. Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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41
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Hens R, Vlugt TJH. Molecular Simulation of Vapor-Liquid Equilibria Using the Wolf Method for Electrostatic Interactions. JOURNAL OF CHEMICAL AND ENGINEERING DATA 2018; 63:1096-1102. [PMID: 30258248 PMCID: PMC6150682 DOI: 10.1021/acs.jced.7b00839] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/29/2017] [Indexed: 06/08/2023]
Abstract
The applicability of the Wolf method for calculating electrostatic interactions is verified for simulating vapor-liquid equilibria of hydrogen sulfide, methanol, and carbon dioxide. Densities, chemical potentials, and critical properties are obtained with Monte Carlo simulations using the Continuous Fractional Component version of the Gibbs Ensemble. Saturated vapor pressures are obtained from NPT simulations. Excellent agreement is found between simulation results and data from literature (simulations using the Ewald summation). It is also shown how to choose the optimal parameters for the Wolf method. Even though the Wolf method requires a large simulation box in the gas phase, due to the lack of screening of electrostatics, one can consider the Wolf method as a suitable alternative to the Ewald summation in VLE calculations.
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42
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Waibel C, Gross J. Modification of the Wolf Method and Evaluation for Molecular Simulation of Vapor–Liquid Equilibria. J Chem Theory Comput 2018; 14:2198-2206. [DOI: 10.1021/acs.jctc.7b01190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Waibel
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
| | - Joachim Gross
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany
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43
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MacDowell LG, Llombart P, Benet J, Palanco JG, Guerrero-Martinez A. Nanocapillarity and Liquid Bridge-Mediated Force between Colloidal Nanoparticles. ACS OMEGA 2018; 3:112-123. [PMID: 31457880 PMCID: PMC6641340 DOI: 10.1021/acsomega.7b01650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/21/2017] [Indexed: 06/10/2023]
Abstract
In this work, we probe the concept of interface tension for ultrathin adsorbed liquid films on the nanoscale by studying the surface fluctuations of films down to the monolayer. Our results show that the spectrum of film height fluctuations of a liquid-vapor surface may be extended to ultrathin films provided we take into account the interactions of the substrate with the surface. Global fluctuations of the film height are described in terms of disjoining pressure, whereas surface deformations that are proportional to the interface area are accounted for by a film thickness-dependent surface tension. As a proof of concept, we model the capillary forces between colloidal nanoparticles held together by liquid bridges. Our results indicate that the classical equations for capillarity follow very precisely down to the nanoscale provided we account for the film height dependence of the surface tension.
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Affiliation(s)
- Luis G. MacDowell
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Pablo Llombart
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Jorge Benet
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Jose G. Palanco
- Departamento
de Materiales y Producción Aeroespacial, ETSI Aeronáuticos, Universidad Politécnica de Madrid, Plaza del Cardenal Cisneros 3, 28040 Madrid, Spain
| | - Andrés Guerrero-Martinez
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, Avda. Complutense s/n, 28040 Madrid, Spain
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44
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Stutzman LB, Escobedo FA, Tester JW. Heat capacities of supercritical fluids via Grand Canonical ensemble simulations. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2017.1355553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Lauren B. Stutzman
- Chemical and Biomolecular Engineering, Cornell Energy Institute, Cornell University, Ithaca, NY, USA
| | - Fernando A. Escobedo
- Chemical and Biomolecular Engineering, Cornell Energy Institute, Cornell University, Ithaca, NY, USA
| | - Jefferson W. Tester
- Chemical and Biomolecular Engineering, Cornell Energy Institute, Cornell University, Ithaca, NY, USA
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45
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Singh SK. Critical temperature estimation of bulk and confined atomic fluid using vapour−liquid interfacial free energy. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2017.1355554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sudhir K. Singh
- Department of Chemical Engineering, Thapar University, Patiala, India
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46
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Yarmolinsky M, Kuklov A. Revisiting universality of the liquid-gas critical point in two dimensions. Phys Rev E 2018; 96:062124. [PMID: 29347405 DOI: 10.1103/physreve.96.062124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Indexed: 11/07/2022]
Abstract
Critical point of liquid-gas (LG) transition does not conform with the paradigm of spontaneous symmetry breaking because there is no broken symmetry in both phases. We revisit the conjecture that this critical point belongs to the Ising class by performing large scale Monte Carlo simulations in two-dimensional free space in combination with the numerical flowgram method. Our main result is that the critical indices do agree with the Onsager values within the error of 1%-2%. This significantly improves the accuracy reported in the literature. The related problem about the role of higher order odd terms in the (real) φ^{4} field model as a mapping of the LG transition is addressed too. The scaling dimension of the φ^{5} term at criticality is shown to be the same as that of the linear one φ. We suggest that the role of all higher order odd terms at criticality is simply in generating the linear field operator with the critical dimension consistent with the Ising universality class.
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Affiliation(s)
- Max Yarmolinsky
- Department of Engineering & Physics, CSI, and the Graduate Center of CUNY, New York 10314, USA
| | - Anatoly Kuklov
- Department of Engineering & Physics, CSI, and the Graduate Center of CUNY, New York 10314, USA
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47
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Wilson BA, Nasrabadi AT, Gelb LD, Nielsen SO. Computing free energies using nested sampling-based approaches. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1416113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Blake A. Wilson
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, TN, USA
| | - Amir T. Nasrabadi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas , Richardson, TX, USA
| | - Lev D. Gelb
- Department of Materials Science and Engineering, The University of Texas at Dallas , Richardson, TX, USA
| | - Steven O. Nielsen
- Department of Chemistry and Biochemistry, The University of Texas at Dallas , Richardson, TX, USA
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48
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Góźdź WT. Investigation of Fluid-Fluid and Solid-Solid Phase Separation of Symmetric Nonadditive Hard Spheres at High Density. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:11727-11732. [PMID: 28826216 DOI: 10.1021/acs.langmuir.7b02228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We have calculated the values of the critical packing fractions for the mixtures of symmetric nonadditive hard spheres at high densities for small values of the nonadditivity parameter. Calculations have been performed for solid-solid and fluid-fluid demixing transitions. A cluster algorithm for Monte Carlo simulations in a semigrand ensemble was used, and the waste recycling method was applied to improve the accuracy of the calculations. The finite size scaling analysis was employed to compute the critical packing fractions for infinite systems with high accuracy.
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Affiliation(s)
- W T Góźdź
- Institute of Physical Chemistry Polish Academy of Sciences , Kasprzaka 44/52, 01-224 Warsaw, Poland
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49
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Singh SK. Corresponding states vapour–liquid phase equilibria of confined square–well fluid. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1304642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sudhir K. Singh
- Department of Chemical Engineering, Thapar University Patiala, Punjab, India
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50
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Evans R, Stewart MC, Wilding NB. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory. J Chem Phys 2017; 147:044701. [DOI: 10.1063/1.4993515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Robert Evans
- H. H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Maria C. Stewart
- H. H. Wills Physics Laboratory, University of Bristol, Royal Fort, Bristol BS8 1TL, United Kingdom
| | - Nigel B. Wilding
- Department of Physics, University of Bath, Bath BA2 7AY, United Kingdom
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