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Peralta A, Odriozola G. A Neural-Network-Optimized Hydrogen Peroxide Pairwise Additive Model for Classical Simulations. J Chem Theory Comput 2023; 19:4172-4181. [PMID: 37306692 PMCID: PMC10921400 DOI: 10.1021/acs.jctc.3c00287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Indexed: 06/13/2023]
Abstract
We have developed an all-atom pairwise additive model for hydrogen peroxide using an optimization procedure based on artificial neural networks (ANNs). The model is based on experimental molecular geometry and includes a dihedral potential that hinders the cis-type configuration and allows for crossing the trans one, defined between the planes that have the two oxygen atoms and each hydrogen. The model's parametrization is achieved by training simple ANNs to minimize a target function that measures the differences between various thermodynamic and transport properties and the corresponding experimental values. Finally, we evaluated a range of properties for the optimized model and its mixtures with SPC/E water, including bulk-liquid properties (density, thermal expansion coefficient, adiabatic compressibility, etc.) and properties of systems at equilibrium (vapor and liquid density, vapor pressure and composition, surface tension, etc.). Overall, we obtained good agreement with experimental data.
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Affiliation(s)
- Alvaro
Ramos Peralta
- Área de Física de Procesos
Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
| | - Gerardo Odriozola
- Área de Física de Procesos
Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
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2
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Prasad S, Gupta M. Solvation of gold nanoparticles passivated with functionalized alkylthiols: A molecular dynamics study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Pauletti M, Rybkin VV, Iannuzzi M. Surface tension of liquids and binary mixtures from molecular dynamics simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:044003. [PMID: 34633303 DOI: 10.1088/1361-648x/ac2e8f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
In this work we assess and extend strategies for calculating surface tension of complex liquids from molecular dynamics simulations: the mechanical route and the instantaneous liquid interface (ILI) approach. The former employs the connection between stress tensor and surface tension, whereas the latter involves computation of instantaneous density field. Whereas the mechanical route is general, the ILI method involves system-dependent parameters restricting its original application to liquid water only. Here we generalize the approach to complex molecular liquids using atomic van der Waals radii. The performance of the approaches is evaluated on two liquid systems: acetonitrile and water-methanol mixture. In addition, we compare the effect of the computational models for interaction potentials based on semi-empirical electronic structure theory and classical force fields on the estimate of the surface tension within both stress tensor and ILI approaches.
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4
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Chen Y, Schultz AJ, Errington JR. Coupled Monte Carlo and Molecular Dynamics Simulations on Interfacial Properties of Antifouling Polymer Membranes. J Phys Chem B 2021; 125:8193-8204. [PMID: 34259529 DOI: 10.1021/acs.jpcb.1c01966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use molecular simulation to study the wetting behavior of antifouling polymer-tethered membranes. We obtain the interfacial properties (e.g., contact angle) of water at various temperatures for five polymer membranes, including a base polysulfone (PSF) membrane and four other PSF membranes grafted with antifouling polymers (two poly(ethylene glycol) (PEG) tethers and two zwitterionic tethers). We implement a coupled Monte Carlo (MC)/molecular dynamics (MD) approach to determine the interface potentials of water on the membrane surfaces in an efficient manner. Within this method, short MC and MD simulations are performed in cycles to collect the surface excess free energy of a thin water film on polymer membrane surfaces. Simulation results show that the grafting of zwitterionic tethers provides a more significant enhancement in the hydrophilicity of the PSF membrane than that of the PEG tethers. Water completely wets the surface of zwitterionic polymer membranes.
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Affiliation(s)
- Yiqi Chen
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York 14260-4200, United States
| | - Andrew J Schultz
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York 14260-4200, United States
| | - Jeffrey R Errington
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, New York 14260-4200, United States
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5
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Prasad S, Chakravarty C. Solvation of LiCl in model liquids with high to low hydrogen bond strengths. J Chem Phys 2017. [DOI: 10.1063/1.4982828] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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6
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Weiss VC. Corresponding-states behavior of SPC/E-based modified (bent and hybrid) water models. J Chem Phys 2017; 146:054506. [DOI: 10.1063/1.4975166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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7
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Shen H, Hao T, Wen J, Tan RR, Zhang FS. Properties of pure water and sodium chloride solutions at high temperatures and pressures: a simulation study. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2014.992019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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8
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Song M, Snyder MA, Mittal J. Effect of molecular structure on fluid transport through carbon nanotubes. Mol Phys 2014. [DOI: 10.1080/00268976.2014.903578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Wen J, Shen X, Shen H, Zhang FS. Hofmeister series and ionic effects of alkali metal ions on DNA conformation transition in normal and less polarised water solvent. Mol Phys 2014. [DOI: 10.1080/00268976.2014.906674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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10
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Prasad S, Chakravarty C. Onset of simple liquid behaviour in modified water models. J Chem Phys 2014; 140:164501. [DOI: 10.1063/1.4870823] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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KATAOKA Y, YAMADA Y. Phase Diagram of a Lennard-Jones System by Molecular Dynamics Simulations. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2014. [DOI: 10.2477/jccj.2013-0023] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Kumar V, Errington JR. Application of the interface potential approach to calculate the wetting properties of a water model system. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.817672] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Machlin ES. Thermodynamics of extensive interfaces between rigid, apolar walls and water. J Chem Phys 2013; 139:134703. [DOI: 10.1063/1.4824020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Musolino N, Trout BL. Insight into the molecular mechanism of water evaporation via the finite temperature string method. J Chem Phys 2013; 138:134707. [PMID: 23574252 DOI: 10.1063/1.4798458] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The process of water's evaporation at its liquid/air interface has proven challenging to study experimentally and, because it constitutes a rare event on molecular time scales, presents a challenge for computer simulations as well. In this work, we simulated water's evaporation using the classical extended simple point charge model water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one O-H bond are oriented outward as it crosses the Gibbs dividing surface. As the water molecule moves further outward through the interfacial region, its local density is higher than the time-averaged density, indicating a local solvation shell that protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining hydrogen bond. At that point, when the final, accepted hydrogen bond is broken, the water molecule is free. We also analyzed which order parameters are most important in the process and in reactive trajectories, and found that the relative orientation of water molecules near the evaporating molecule, and the number of accepted hydrogen bonds, were important variables in reactive trajectories and in kinetic descriptions of the process.
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Affiliation(s)
- Nicholas Musolino
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Rm. E19-502, Cambridge, Massachusetts 02144, USA
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Lasich M, Johansson EL, Ramjugernath D. Monte Carlo simulations of water solubility and structures in poly(difluoromethylene). MOLECULAR SIMULATION 2012. [DOI: 10.1080/08927022.2012.731505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Head-Gordon T, Lynden-Bell RM, Dowdle JR, Rossky PJ. Predicting cavity formation free energy: how far is the Gaussian approximation valid? Phys Chem Chem Phys 2012; 14:6996-7004. [PMID: 22495173 DOI: 10.1039/c2cp00046f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We examine the range of validity of the Gaussian model for various water-like liquids whose intermolecular potentials differ from SPC/E water, to provide insight into the temperature dependence of the hydrophobic effect for small hard sphere solutes. We find that low compressibility liquids that have more close-packed network structures show much larger deviations from Gaussian fluctuations for low or zero occupancies relative to more compressible fluids with more open networks. Water appears to be a unique molecular fluid in possessing equilibrium density fluctuations that are faithfully described by the Gaussian theory. We ascribe this success to the fact, shown here, that the orientational correlations near a small hard sphere solute involve remarkably little reorganization from the bulk, which is a consequence of water's low solvent reorganization enthalpy and entropy.
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Affiliation(s)
- T Head-Gordon
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
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WANG JUN, ZENG XIAOCHENG. COMPUTER SIMULATION OF LIQUID–VAPOR INTERFACIAL TENSION: LENNARD-JONES FLUID AND WATER REVISITED. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633609005027] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We review several commonly used simulation methods for computing liquid–vapor surface tension and associated theoretical treatments of the long-range correction for inhomogeneous systems. Prototype model systems considered in this review are the Lennard-Jones (LJ) fluid and the SPC/E model water. In addition, we examine a variety of factors that can affect calculation of the surface tension γ via the mechanical approach (i.e. using either KB or IK method). It is found that for the LJ fluid, the size of simulation box and the number of particles in the system can have notable effects on the computed surface tension. For SPC/E water, the Ewald parameters can influence computed surface tensions (γ) as well, e.g., very small Ewald parameters tend to overestimate γ. It is also found that the IK method consistently gives γ that are 0.6 - 0.9 mN/m greater than γ computed based on the KB method. When computing the first reciprocal–space contribution to the surface tension, the Ghoufi's strategy gives rise to more sensible profile of pressure difference PN(z)-PT(z) than the Alejandre's strategy although both strategies result in nearly the same average surface tension through the integration of PN(z)-PT(z).
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Affiliation(s)
- JUN WANG
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - XIAO CHENG ZENG
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
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Nezbeda I, Jirsák J. Water and aqueous solutions: simple non-speculative model approach. Phys Chem Chem Phys 2011; 13:19689-703. [PMID: 21952227 DOI: 10.1039/c1cp21903k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Different ways of molecular modeling of water are analyzed and their similarities and differences identified. An up-to-date summary of achievements of a general approach to common rigid site-site interaction models of molecular fluids applied to water and aqueous solutions is then presented and discussed. The method is based on considering only a short-range part of a total realistic potential (such as SPC/E or TIPxP) which determines the structure of water (and fluids in general). A simplification of the interactions at short intermolecular separations leads then to simple models, called primitive models. Quite accurate results in an analytic form for the thermodynamic properties of the models are obtained using the thermodynamic perturbation theory. It is shown that the properly constructed primitive models reproduce, qualitatively, anomalies of pure water and basic characteristics of hydrophobic hydration. The concept of an extended excluded volume, based on pseudo-hard bodies, is introduced and exemplified by considering the partial molar volume of apolar solutes. Potential future development towards a theory of water based on the primitive models as a reference with the long-range contributions added as a perturbation is discussed.
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Affiliation(s)
- Ivo Nezbeda
- Chemistry Department, Faculty of Science, J. E. Purkinje University, Ústí nad Labem, Czech Republic.
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19
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Sakamaki R, Sum AK, Narumi T, Yasuoka K. Molecular dynamics simulations of vapor/liquid coexistence using the nonpolarizable water models. J Chem Phys 2011; 134:124708. [DOI: 10.1063/1.3574038] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Lynden-Bell RM, Giovambattista N, Debenedetti PG, Head-Gordon T, Rossky PJ. Hydrogen bond strength and network structure effects on hydration of non-polar molecules. Phys Chem Chem Phys 2011; 13:2748-57. [DOI: 10.1039/c0cp01701a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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da Silva JAB, Moreira FGB, dos Santos VML, Longo RL. Hydrogen bond networks in water and methanol with varying interaction strengths. Phys Chem Chem Phys 2011; 13:593-603. [DOI: 10.1039/c0cp01204a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Lynden-Bell RM. Towards understanding water: simulation of modified water models. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010; 22:284107. [PMID: 21399279 DOI: 10.1088/0953-8984/22/28/284107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The unusual properties of liquid water have been attributed to factors including hydrogen bonds, the presence of a local tetrahedral network, or the high number density. Most of the properties of water can be reproduced in simulations using simple potential models with site-site pairwise interactions. Although in real water the factors listed above cannot be separated, one may construct liquids from modified water models ('not-waters') in which these factors are altered independently in a controlled way. With various collaborators we have studied the changes in liquid properties, anomalies and solvation which result from various modifications.
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Affiliation(s)
- R M Lynden-Bell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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23
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Alejandre J, Chapela GA. The dipole moment distribution on water is improved by using large flexibility and large bending angle. Mol Phys 2010. [DOI: 10.1080/00268970903563451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Gustavo A. Chapela
- b Departamento de Física , Universidad Autónoma Metropolitana-Iztapalapa , Av. San Rafael Atlixco 186, Col. Vicentina, 09340 México D.F., México
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Alejandre J, Chapela GA, Bresme F, Hansen JP. The short range anion-H interaction is the driving force for crystal formation of ions in water. J Chem Phys 2009; 130:174505. [DOI: 10.1063/1.3124184] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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López-Lemus J, Chapela GA, Alejandre J. Effect of flexibility on surface tension and coexisting densities of water. J Chem Phys 2008; 128:174703. [DOI: 10.1063/1.2907845] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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26
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Mendoza FN, López-Rendón R, López-Lemus J, Cruz J, Alejandre J. Surface tension of hydrocarbon chains at the liquid–vapour interface. Mol Phys 2008. [DOI: 10.1080/00268970802119694] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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27
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Head-Gordon T, Lynden-Bell RM. Hydrophobic solvation of Gay–Berne particles in modified water models. J Chem Phys 2008; 128:104506. [DOI: 10.1063/1.2837289] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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