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Becker M, Loche P, Rezaei M, Wolde-Kidan A, Uematsu Y, Netz RR, Bonthuis DJ. Multiscale Modeling of Aqueous Electric Double Layers. Chem Rev 2024; 124:1-26. [PMID: 38118062 PMCID: PMC10785765 DOI: 10.1021/acs.chemrev.3c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 11/17/2023] [Accepted: 11/30/2023] [Indexed: 12/22/2023]
Abstract
From the stability of colloidal suspensions to the charging of electrodes, electric double layers play a pivotal role in aqueous systems. The interactions between interfaces, water molecules, ions and other solutes making up the electrical double layer span length scales from Ångströms to micrometers and are notoriously complex. Therefore, explaining experimental observations in terms of the double layer's molecular structure has been a long-standing challenge in physical chemistry, yet recent advances in simulations techniques and computational power have led to tremendous progress. In particular, the past decades have seen the development of a multiscale theoretical framework based on the combination of quantum density functional theory, force-field based simulations and continuum theory. In this Review, we discuss these theoretical developments and make quantitative comparisons to experimental results from, among other techniques, sum-frequency generation, atomic-force microscopy, and electrokinetics. Starting from the vapor/water interface, we treat a range of qualitatively different types of surfaces, varying from soft to solid, from hydrophilic to hydrophobic, and from charged to uncharged.
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Affiliation(s)
| | - Philip Loche
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
- Laboratory
of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Majid Rezaei
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
- Institute
of Theoretical Chemistry, Ulm University, 89081 Ulm, Germany
| | | | - Yuki Uematsu
- Department
of Physics and Information Technology, Kyushu
Institute of Technology, 820-8502 Iizuka, Japan
- PRESTO,
Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Roland R. Netz
- Fachbereich
Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Douwe Jan Bonthuis
- Institute
of Theoretical and Computational Physics, Graz University of Technology, 8010 Graz, Austria
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2
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Janicki TD, Van Vleet MJ, Schmidt JR. Development and Implementation of Atomically Anisotropic First-Principles Force Fields: A Benzene Case Study. J Phys Chem A 2023; 127:1736-1749. [PMID: 36780209 DOI: 10.1021/acs.jpca.2c07244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
π-interactions are an important motif in chemical and biochemical systems. However, due to their anisotropic electron densities and complex balance of intermolecular interactions, aromatic molecules represent an ongoing challenge for accurate and transferable force field development. Historically, ab initio force fields for aromatics have not exhibited good accuracy with respect to bulk properties or have only been used to study gas-phase dimers. Using benzene as a proof of concept, herein we show how our own ab initio MASTIFF force field incorporates an atomically anisotropic description of intermolecular interactions to yield an accurate and robust model for aromatic interactions irrespective of phase. Compared to existing models, the MASTIFF benzene force field not only is accurate for liquid phase properties but also offers transferability to the gas and solid phases. Additionally, we introduce a computationally efficient OpenMM plugin which enables customizable anisotropic intermolecular functional forms and which can be generically used in any MD simulation where a model for nonspherical atomic features is required. Overall, our results demonstrate the importance of atomic-level anisotropy in enabling next-generation ab initio force field development.
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Affiliation(s)
- Tesia D Janicki
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mary J Van Vleet
- Department of Chemistry and Biochemistry, Spelman College, 350 Spelman Ln SW, Atlanta, Georgia 30314, United States
| | - J R Schmidt
- Department of Chemistry, University of Wisconsin─Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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3
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Wang J, Zheng Y, Zhang H, Ye H. Machine learning-generated TIP4P-BGWT model for liquid and supercooled water. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Ye HF, Wang J, Zheng YG, Zhang HW, Chen Z. Machine learning for reparameterization of four-site water models: TIP4P-BG and TIP4P-BGT. Phys Chem Chem Phys 2021; 23:10164-10173. [PMID: 33951125 DOI: 10.1039/d0cp05831a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Parameterizing an effective water model is a challenging issue because of the difficulty in maintaining a comprehensive balance among the diverse physical properties of water with a limited number of parameters. The advancement in machine learning provides a promising path to search for a reliable set of parameters. Based on the TIP4P water model, hence, about 6000 molecular dynamics (MD) simulations for pure water at 1 atm and in the range of 273-373 K are conducted here as the training data. The back-propagation (BP) neural network is then utilized to construct an efficient mapping between the model parameters and four crucial physical properties of water, including the density, vaporization enthalpy, self-diffusion coefficient and viscosity. Without additional time-consuming MD simulations, this mapping operation could result in sufficient and accurate data for high-population genetic algorithm (GA) to optimize the model parameters as much as possible. Based on the proposed parameterizing strategy, TIP4P-BG (a conventional four-site water model) and TIP4P-BGT (an advanced model with temperature-dependent parameters) are established. Both the water models exhibit excellent performance with a reasonable balance among the four crucial physical properties. The relevant mean absolute percentage errors are 3.53% and 3.08%, respectively. Further calculations on the temperature of maximum density, isothermal compressibility, thermal expansion coefficient, radial distribution function and surface tension are also performed and the resulting values are in good agreement with the experimental values. Through this water modeling example, the potential of the proposed data-driven machine learning procedure has been demonstrated for parameterizing a MD-based material model.
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Affiliation(s)
- Hong-Fei Ye
- International Research Center for Computational Mechanics, State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Faculty of Vehicle Engineering and Mechanics, Dalian University of Technology, Dalian 116024, P. R. China.
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5
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Teng X, Liu B, Ichiye T. Understanding how water models affect the anomalous pressure dependence of their diffusion coefficients. J Chem Phys 2020; 153:104510. [PMID: 32933292 DOI: 10.1063/5.0021472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The self-diffusion coefficient of water shows an anomalous increase with increasing hydrostatic pressure up to a broad maximum (PmD) near 1 kbar at 298 K, which has been attributed to pressure effects on the tetrahedral hydrogen bond network of water. Moreover, the ability of a water model to reproduce anomalous properties of water is a signature that it is reproducing the network. Here, water was simulated between 1 bar and 5 kbar using three water models, two four-site (with all charges in the molecular plane) and one single-site multipole (which accounts for out-of-molecular plane charge), that have reasonable pressure-temperature properties. For these three models, the diffusion coefficients display a maximum in the pressure dependence and the radial distribution functions show good agreement with the limited experimental structural data at high pressure that are available. In addition, a variety of properties associated with the network are examined, including hydrogen bond lifetimes and occupancies, three-body angle distributions, and tetrahedral order parameters. Results suggest that the initial increasing diffusion with pressure is because hydrogen bonds are distorted and thus weakened by pressure, but above PmD, the hydrogen bonds are weakened to the point it behaves more like a normal liquid. In other words, the PmD may be a measure of the angular strength of hydrogen bonds. In addition, since the four-site models over-predict the values of PmD while the multipole model under-predicts it, out-of-plane charge may improve four-site models.
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Affiliation(s)
- Xiaojing Teng
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Bailang Liu
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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6
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Abstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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7
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile. Int J Mol Sci 2019; 20:E1452. [PMID: 30909394 PMCID: PMC6470811 DOI: 10.3390/ijms20061452] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/04/2022] Open
Abstract
Determining the effects of extreme conditions on proteins from "extremophilic" and mesophilic microbes is important for understanding how life adapts to living at extremes as well as how extreme conditions can be used for sterilization and food preservation. Previous molecular dynamics simulations of dihydrofolate reductase (DHFR) from a psychropiezophile (cold- and pressure-loving), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec), at various pressures and temperatures indicate that atomic fluctuations, which are important for enzyme function, increase with both temperature and pressure. Here, the factors that cause increases in atomic fluctuations in the simulations are examined. The fluctuations increase with temperature not only because of greater thermal energy and thermal expansion of the protein but also because hydrogen bonds between protein atoms are weakened. However, the increase in fluctuations with pressure cannot be due to thermal energy, which remains constant, nor the compressive effects of pressure, but instead, the hydrogen bonds are also weakened. In addition, increased temperature causes larger increases in fluctuations of the loop regions of MpDHFR than EcDHFR, and increased pressure causes both increases and decreases in fluctuations of the loops, which differ between the two.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
| | - Jocelyn M Rodgers
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
| | - Russell J Hemley
- Department of Civil and Environmental Engineering, George Washington University, Washington, DC 20052, USA.
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
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Tsimpanogiannis IN, Moultos OA, Franco LFM, Spera MBDM, Erdős M, Economou IG. Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1511903] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ioannis N. Tsimpanogiannis
- Environmental Research Laboratory, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
| | - Othonas A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Luís F. M. Franco
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | | | - Máté Erdős
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, The Netherlands
| | - Ioannis G. Economou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research “Demokritos”, Aghia Paraskevi Attikis, Greece
- Chemical Engineering Program, Texas A&M University at Qatar, Doha, Qatar
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9
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Teng X, Huang Q, Dharmawardhana CC, Ichiye T. Diffusion of aqueous solutions of ionic, zwitterionic, and polar solutes. J Chem Phys 2018; 148:222827. [PMID: 29907024 DOI: 10.1063/1.5023004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The properties of aqueous solutions of ionic, zwitterionic, and polar solutes are of interest to many fields. For instance, one of the many anomalous properties of aqueous solutions is the behavior of water diffusion in different monovalent salt solutions. In addition, solutes can affect the stabilities of macromolecules such as proteins in aqueous solution. Here, the diffusivities of aqueous solutions of sodium chloride, potassium chloride, tri-methylamine oxide (TMAO), urea, and TMAO-urea are examined in molecular dynamics simulations. The decrease in the diffusivity of water with the concentration of simple ions and urea can be described by a simple model in which the water molecules hydrogen bonded to the solutes are considered to diffuse at the same rate as the solutes, while the remainder of the water molecules are considered to be bulk and diffuse at almost the same rate as pure water. On the other hand, the decrease in the diffusivity of water with the concentration of TMAO is apparently affected by a decrease in the diffusion rate of the bulk water molecules in addition to the decrease due to the water molecules hydrogen bonded to TMAO. In other words, TMAO enhances the viscosity of water, while urea barely affects it. Overall, this separation of water molecules into those that are hydrogen bonded to solute and those that are bulk can provide a useful means of understanding the short- and long-range effects of solutes on water.
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Affiliation(s)
- Xiaojing Teng
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | | | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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10
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Dharmawardhana CC, Ichiye T. Building better water models using the shape of the charge distribution of a water molecule. J Chem Phys 2018; 147:194103. [PMID: 29166096 DOI: 10.1063/1.4986070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.
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Affiliation(s)
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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11
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Demerdash O, Wang L, Head‐Gordon T. Advanced models for water simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1355] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Omar Demerdash
- Kenneth S. Pitzer Center for Theoretical Chemistry University of California Berkeley CA USA
- Department of Chemistry University of California Berkeley CA USA
| | - Lee‐Ping Wang
- Department of Chemistry University of California, Davis Davis CA USA
| | - Teresa Head‐Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry University of California Berkeley CA USA
- Department of Chemistry University of California Berkeley CA USA
- Department of Bioengineering University of California Berkeley CA USA
- Department of Chemical and Biomolecular Engineering University of California Berkeley CA USA
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12
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Onufriev AV, Izadi S. Water models for biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1347] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Alexey V. Onufriev
- Department of Physics; Virginia Tech; Blacksburg VA USA
- Department of Computer Science; Virginia Tech; Blacksburg VA USA
- Center for Soft Matter and Biological Physics; Virginia Tech; Blacksburg VA USA
| | - Saeed Izadi
- Early Stage Pharmaceutical Development; Genentech Inc.; South San Francisco, CA USA
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Huang Q, Rodgers JM, Hemley RJ, Ichiye T. Extreme biophysics: Enzymes under pressure. J Comput Chem 2017; 38:1174-1182. [PMID: 28101963 PMCID: PMC6334844 DOI: 10.1002/jcc.24737] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 12/05/2016] [Accepted: 01/03/2017] [Indexed: 01/16/2023]
Abstract
A critical question about piezophilic (pressure-loving) microbes is how their constituent molecules maintain function under high pressure. Here, factors are examined that may lead to the increased activity under pressure in dihydrofolate reductase from the piezophilic Moritella profunda compared to the homologous enzyme from the mesophilic Escherichia coli. Molecular dynamics simulations are performed at various temperatures and pressures to examine how pressure affects the flexibility of the enzymes from these two microbes, since both stability and flexibility are necessary for enzyme activity. The results suggest that collective motions on the 10-ns timescale are responsible for the flexibility necessary for "corresponding states" activity at the growth conditions of the parent organism. In addition, the results suggest that while the lower stability of many enzymes from deep-sea microbes may be an adaptation for greater flexibility at low temperatures, high pressure may enhance their adaptation to low temperatures. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Qi Huang
- Department of Chemistry, Georgetown University, Washington, DC, USA, 20057
| | - Jocelyn M. Rodgers
- Department of Chemistry, Georgetown University, Washington, DC, USA, 20057; Geophysical Laboratory, Carnegie Institution for Science, Washington, DC, USA, 20015
| | - Russell J. Hemley
- Department of Civil and Environmental Engineering, George Washington University, Washington, DC, USA, 20052
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, USA, 20057
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14
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Rodgers JM, Ichiye T. Multipole moments of water molecules and the aqueous solvation of monovalent ions. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2016.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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