1
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Simulations of dielectric constants and viscosities of organic electrolytes by quantum mechanics and molecular dynamics. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113288] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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2
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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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3
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Cisneros G, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chem Rev 2016; 116:7501-28. [PMID: 27186804 PMCID: PMC5450669 DOI: 10.1021/acs.chemrev.5b00644] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Indexed: 12/17/2022]
Abstract
Almost 50 years have passed from the first computer simulations of water, and a large number of molecular models have been proposed since then to elucidate the unique behavior of water across different phases. In this article, we review the recent progress in the development of analytical potential energy functions that aim at correctly representing many-body effects. Starting from the many-body expansion of the interaction energy, specific focus is on different classes of potential energy functions built upon a hierarchy of approximations and on their ability to accurately reproduce reference data obtained from state-of-the-art electronic structure calculations and experimental measurements. We show that most recent potential energy functions, which include explicit short-range representations of two-body and three-body effects along with a physically correct description of many-body effects at all distances, predict the properties of water from the gas to the condensed phase with unprecedented accuracy, thus opening the door to the long-sought "universal model" capable of describing the behavior of water under different conditions and in different environments.
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Affiliation(s)
| | - Kjartan Thor Wikfeldt
- Science
Institute, University of Iceland, VR-III, 107, Reykjavik, Iceland
- Department
of Physics, Albanova, Stockholm University, S-106 91 Stockholm, Sweden
| | - Lars Ojamäe
- Department
of Chemistry, Linköping University, SE-581 83 Linköping, Sweden
| | - Jibao Lu
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Yao Xu
- Lehrstuhl
Physikalische Chemie II, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Hedieh Torabifard
- Department
of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Albert P. Bartók
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Gábor Csányi
- Engineering
Laboratory, University of Cambridge, Trumpington Street, Cambridge CB21PZ, United Kingdom
| | - Valeria Molinero
- Department
of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, United States
| | - Francesco Paesani
- Department
of Chemistry and Biochemistry, University
of California San Diego, La Jolla, California 92093, United States
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4
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Abstract
Hydrogen bond directionality in the water dimer is explained on the basis of symmetry-adapted intermolecular perturbation theory which directly separates the intermolecular interaction energy into four physically interpretable components: electrostatics, exchange-repulsion, dispersion, and induction. Analysis of these four main contributions to the binding energy allows a deeper understanding of the dominant factors ruling the mutual arrangement of the two monomers. A preference for the linear configuration is shown to be due to a subtle interplay of all four energy components. While the first-order terms, electrostatic and exchange-repulsion, almost perfectly cancel each other near the equilibrium geometry of the dimer, the importance of the second- and higher-order terms, induction and dispersion, becomes evident.
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Affiliation(s)
- Maxim Tafipolsky
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Campus Hubland Nord , Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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5
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Tafipolsky M, Ansorg K. Toward a Physically Motivated Force Field: Hydrogen Bond Directionality from a Symmetry-Adapted Perturbation Theory Perspective. J Chem Theory Comput 2016; 12:1267-79. [DOI: 10.1021/acs.jctc.5b01057] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maxim Tafipolsky
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
| | - Kay Ansorg
- Institut
für Physikalische
und Theoretische Chemie, Universität Würzburg, Campus
Hubland Nord, Emil-Fischer-Strasse 42, D-97074 Würzburg, Germany
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6
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Loboda O, Ingrosso F, Ruiz-López MF, Szalewicz K, Millot C. Geometry-dependent distributed polarizability models for the water molecule. J Chem Phys 2016; 144:034304. [PMID: 26801031 DOI: 10.1063/1.4939519] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successively occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.
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Affiliation(s)
- Oleksandr Loboda
- Université de Lorraine, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506, France
| | - Francesca Ingrosso
- Université de Lorraine, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506, France
| | - Manuel F Ruiz-López
- Université de Lorraine, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506, France
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Claude Millot
- Université de Lorraine, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506, France
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7
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Ekesan S, Herzfeld J. Pointillist rendering of electron charge and spin density suffices to replicate trends in atomic properties. Proc Math Phys Eng Sci 2015. [DOI: 10.1098/rspa.2015.0370] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The monotonic and non-monotonic variations of atomic properties within and between the rows of the periodic table underlie our understanding of chemistry and accounting for these variations has been a signature strength of quantum mechanics (QM). However, the computational burden of QM motivates the development of more efficient means of describing electrons and reactivity. The recently developed LEWIS
•
model incorporates lessons learnt from QM into a force field that includes electrons as explicit pseudo-classical particles. Here, we extend LEWIS
•
across the 2
p
and 3
p
elements, and show that it is capable of reproducing both monotonic and non-monotonic variations of chemically important atomic properties in a cost-effective manner. An indicator of the strength of the construct is the ability of pairwise potentials trained on ionization energies and the order of spin configurations to predict atomic polarizabilities. In this manner, some insights of QM are uncoupled from its onerous computational burden.
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8
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Jurij R, Per L. MOLSIM: A modular molecular simulation software. J Comput Chem 2015; 36:1259-74. [PMID: 25994597 PMCID: PMC5033024 DOI: 10.1002/jcc.23919] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/23/2015] [Accepted: 03/26/2015] [Indexed: 11/06/2022]
Abstract
The modular software MOLSIM for all-atom molecular and coarse-grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross-linked networks; (3) long-range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction-field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many-body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user-providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks.
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Affiliation(s)
- Reščič Jurij
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, PO Box 537, SI-1001, Ljubljana, Slovenia
| | - Linse Per
- Department of Chemistry, Physical Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
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9
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Daub CD, Åstrand PO, Bresme F. Lithium Ion–Water Clusters in Strong Electric Fields: A Quantum Chemical Study. J Phys Chem A 2015; 119:4983-92. [DOI: 10.1021/acs.jpca.5b01822] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christopher D. Daub
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU) NO-7491, Trondheim, Norway
| | - Per-Olof Åstrand
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU) NO-7491, Trondheim, Norway
| | - Fernando Bresme
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU) NO-7491, Trondheim, Norway
- Department
of Chemistry, Imperial College London SW7 2AZ, London, United Kingdom
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10
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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11
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Ren P, Chun J, Thomas DG, Schnieders MJ, Marucho M, Zhang J, Baker NA. Biomolecular electrostatics and solvation: a computational perspective. Q Rev Biophys 2012; 45:427-91. [PMID: 23217364 PMCID: PMC3533255 DOI: 10.1017/s003358351200011x] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.
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Affiliation(s)
- Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin
| | | | | | | | - Marcelo Marucho
- Department of Physics and Astronomy, The University of Texas at San Antonio
| | - Jiajing Zhang
- Department of Biomedical Engineering, The University of Texas at Austin
| | - Nathan A. Baker
- To whom correspondence should be addressed. Pacific Northwest National Laboratory, PO Box 999, MSID K7-29, Richland, WA 99352. Phone: +1-509-375-3997,
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12
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Georg HC, Canuto S. Electronic Properties of Water in Liquid Environment. A Sequential QM/MM Study Using the Free Energy Gradient Method. J Phys Chem B 2012; 116:11247-54. [DOI: 10.1021/jp304201b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Herbert C. Georg
- Instituto de Física, Universidade Federal de Goiás, CP 131, 74001-970, Goiânia,
GO, Brazil
| | - Sylvio Canuto
- Instituto
de Física, Universidade de São Paulo, CP 66318, 05314-970, São
Paulo, SP, Brazil
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13
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Pratas F, Sousa L, Dieterich JM, Mata RA. Computation of Induced Dipoles in Molecular Mechanics Simulations Using Graphics Processors. J Chem Inf Model 2012; 52:1159-66. [DOI: 10.1021/ci200564x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Frederico Pratas
- INESC-ID/IST, Technical University of Lisbon, Rua Alves Redol, 9, 1000-029 Lisboa,
Portugal
| | - Leonel Sousa
- INESC-ID/IST, Technical University of Lisbon, Rua Alves Redol, 9, 1000-029 Lisboa,
Portugal
| | - Johannes M. Dieterich
- Institut für
Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
| | - Ricardo A. Mata
- Institut für
Physikalische
Chemie, Universität Göttingen, Tammannstrasse 6, D-37077 Göttingen, Germany
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14
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15
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Patuwo MY, Bettens RP. Monte Carlo simulation of several biologically relevant molecules and zwitterions in water. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2011.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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16
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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17
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Schmidt RG, Brickmann J. Molecular dynamics simulation of the proton transport in water. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19971011205] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GNI, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. J Phys Chem B 2010; 114:2549-64. [PMID: 20136072 PMCID: PMC2918242 DOI: 10.1021/jp910674d] [Citation(s) in RCA: 945] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular force fields have been approaching a generational transition over the past several years, moving away from well-established and well-tuned, but intrinsically limited, fixed point charge models toward more intricate and expensive polarizable models that should allow more accurate description of molecular properties. The recently introduced AMOEBA force field is a leading publicly available example of this next generation of theoretical model, but to date, it has only received relatively limited validation, which we address here. We show that the AMOEBA force field is in fact a significant improvement over fixed charge models for small molecule structural and thermodynamic observables in particular, although further fine-tuning is necessary to describe solvation free energies of drug-like small molecules, dynamical properties away from ambient conditions, and possible improvements in aromatic interactions. State of the art electronic structure calculations reveal generally very good agreement with AMOEBA for demanding problems such as relative conformational energies of the alanine tetrapeptide and isomers of water sulfate complexes. AMOEBA is shown to be especially successful on protein-ligand binding and computational X-ray crystallography where polarization and accurate electrostatics are critical.
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Affiliation(s)
- Jay W Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, Missouri 63110, USA
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19
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Walsh TR, Liang T. A multipole-based water potential with implicit polarization for biomolecular simulations. J Comput Chem 2009; 30:893-9. [PMID: 18785240 DOI: 10.1002/jcc.21111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A new water potential, DMIP (distributed multipoles, implicit polarization), is constructed using distributed multipoles to describe the electrostatic interactions, while accounting for polarization implicitly. In this procedure, small clusters are randomly sampled from atomistic simulations of bulk water using the AMOEBA (Ren and Ponder, J Comput Chem 2002, 23, 1497) potential. The multipole moments of the central water in each cluster are obtained from ab initio densities for each cluster, and the moments are then averaged over all clusters. Properties of bulk water calculated using DMIP compare favorably with existing data from AMOEBA simulations and experiment, with a conservative estimate of reduction in compute time of roughly 40%. The implicit force-field is also shown to work compatibly with existing polarizable multipole-based force-fields for biomolecules.
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Affiliation(s)
- T R Walsh
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry, CV4 7AL, United Kingdom.
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20
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Yan S, Lee SJ, Kang S, Lee JY. Computational Approaches in Molecular Recognition, Self-assembly, Electron Transport, and Surface Chemistry. Supramol Chem 2007. [DOI: 10.1080/10610270701261547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Shihai Yan
- a Department of Chemistry , Sungkyunkwan University , Suwon, 440-746, South Korea
| | - Sang Joo Lee
- b Korea Institute of Science and Technology Information, Center for Computational Biology and Bioinformatics , 52, Eoeun-dong, Yuseong, Daejeon, 305-806, South Korea
| | - Sunwoo Kang
- a Department of Chemistry , Sungkyunkwan University , Suwon, 440-746, South Korea
| | - Jin Yong Lee
- a Department of Chemistry , Sungkyunkwan University , Suwon, 440-746, South Korea
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21
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Sylvester-Hvid KO, Mikkelsen KV, Nymand TM, Astrand PO. Refractive index of liquid water in different solvent models. J Phys Chem A 2007; 109:905-14. [PMID: 16838963 DOI: 10.1021/jp046556g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a combined molecular dynamics/quantum chemical perturbation method for calculating the refractive index of liquid water at different temperatures. We compare results of this method with the refractive index obtained from other solvent models. The best agreement with the experimental refractive index of liquid water and its temperature dependence is obtained using correlated gas-phase polarizabilities in the classical Lorentz-Lorenz expression. Also, the iterative self-consistent reaction field approach in the semicontinuum implementation matches the experimental refractive index reasonably well.
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Affiliation(s)
- Kristian O Sylvester-Hvid
- Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark.
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22
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Wallqvist A, Mountain RD. Molecular Models of Water: Derivation and Description. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125908.ch4] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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23
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Solheim H, Ruud K, Astrand PO. Atomic dipole moments calculated using analytical molecular second-moment gradients. J Chem Phys 2004; 120:10368-78. [PMID: 15268064 DOI: 10.1063/1.1738631] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have implemented analytical second-moment gradients for Hartree-Fock and multiconfigurational self-consistent-field wave functions. The code is used to calculate atomic dipole moments based on the generalized atomic polar tensor (GAPT) formalism [Phys. Rev. Lett. 62, 1469 (1989)], and the proposal of Dinur and Hagler (DH) for the calculation of atomic multipoles [J. Chem. Phys. 91, 2949 (1989)]. Both approaches display smooth basis-set convergence toward a well-defined basis-set limit and give reasonable electron correlation effects on the calculated atomic properties. However, the atomic charges and atomic dipole moments obtained from the GAPT partitioning scheme are unable to provide even qualitatively meaningful molecular quadrupole moments for some molecules, and thus the atomic multipole moments calculated in this scheme cannot be considered well suited for analyzing the electron density in molecules and for calculating intermolecular interaction energies. In contrast, the DH approach gives atomic charges and dipole moments that by definition exactly reproduce the molecular quadrupole moments. The approach of DH is, however, restricted to planar molecules and thus suffers from not being applicable to molecules of arbitrary shape. Both the GAPT and DH approaches give rather poor results for octupole and hexadecapole moments, indicating that at least atomic quadrupole moments are required for an accurate representation of the molecular charge distribution in terms of atomic electric moments.
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Affiliation(s)
- Harald Solheim
- Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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24
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Ren P, Ponder JW. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation. J Phys Chem B 2003. [DOI: 10.1021/jp027815+] [Citation(s) in RCA: 1110] [Impact Index Per Article: 52.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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26
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Honda K. An effective potential function with enhanced charge-transfer-type interaction for hydrogen-bonding liquids. J Chem Phys 2002. [DOI: 10.1063/1.1495851] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Goldman N, Fellers RS, Brown MG, Braly LB, Keoshian CJ, Leforestier C, Saykally RJ. Spectroscopic determination of the water dimer intermolecular potential-energy surface. J Chem Phys 2002. [DOI: 10.1063/1.1476932] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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28
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Stern HA, Berne BJ. Quantum effects in liquid water: Path-integral simulations of a flexible and polarizable ab initio model. J Chem Phys 2001. [DOI: 10.1063/1.1407287] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stern HA, Rittner F, Berne BJ, Friesner RA. Combined fluctuating charge and polarizable dipole models: Application to a five-site water potential function. J Chem Phys 2001. [DOI: 10.1063/1.1376165] [Citation(s) in RCA: 248] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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NYMAND THOMASM, LINSE PER, ÅSTRAND PEROLOF. A comparison of effective and polarizable intermolecular potentials in simulations: liquid water as a test case. Mol Phys 2001. [DOI: 10.1080/00268970010015605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Bursulaya BD, Brooks CL. Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models. J Phys Chem B 2000. [DOI: 10.1021/jp0027602] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Badry D. Bursulaya
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Charles L. Brooks
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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Engkvist O, Astrand PO, Karlström G. Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations. Chem Rev 2000; 100:4087-108. [PMID: 11749341 DOI: 10.1021/cr9900477] [Citation(s) in RCA: 153] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- O Engkvist
- Department of Theoretical Chemistry, Chemical Centre, University of Lund, P.O.B. 124, S-221 00 Lund, Sweden
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Wormer PE, van Der Avoird A. Intermolecular potentials, internal motions, and spectra of van der waals and hydrogen-bonded complexes. Chem Rev 2000; 100:4109-44. [PMID: 11749342 DOI: 10.1021/cr990046e] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P E Wormer
- Institute of Theoretical Chemistry, NSR Center, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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Nymand TM, Linse P. Molecular dynamics simulations of polarizable water at different boundary conditions. J Chem Phys 2000. [DOI: 10.1063/1.481200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nymand TM, Linse P. Ewald summation and reaction field methods for potentials with atomic charges, dipoles, and polarizabilities. J Chem Phys 2000. [DOI: 10.1063/1.481216] [Citation(s) in RCA: 152] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fellers RS, Braly LB, Saykally RJ, Leforestier C. Fully coupled six-dimensional calculations of the water dimer vibration-rotation-tunneling states with split Wigner pseudospectral approach. II. Improvements and tests of additional potentials. J Chem Phys 1999. [DOI: 10.1063/1.478535] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Sabo D, Bačić Z, Graf S, Leutwyler S. Rotational constants of all H/D substituted water trimers: Coupling of intermolecular torsional and symmetric stretching modes. J Chem Phys 1999. [DOI: 10.1063/1.478473] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Sabo D, Bačić Z, Graf S, Leutwyler S. Four-dimensional model calculation of torsional levels of cyclic water tetramer. J Chem Phys 1998. [DOI: 10.1063/1.477159] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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JEAN-CHRISTOPHE SOETENS MARILIA T.. RESEARCH NOTE Static dielectric constant of the polarizable NCC water model. Mol Phys 1998. [DOI: 10.1080/002689798168097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Liu YP, Kim K, Berne BJ, Friesner RA, Rick SW. Constructing ab initio force fields for molecular dynamics simulations. J Chem Phys 1998. [DOI: 10.1063/1.475886] [Citation(s) in RCA: 115] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Bursulaya BD, Kim HJ. Generalized molecular mechanics including quantum electronic structure variation of polar solvents. I. Theoretical formulation via a truncated adiabatic basis set description. J Chem Phys 1998. [DOI: 10.1063/1.475724] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Millot C, Soetens JC, Martins Costa MTC, Hodges MP, Stone AJ. Revised Anisotropic Site Potentials for the Water Dimer and Calculated Properties. J Phys Chem A 1998. [DOI: 10.1021/jp972578+] [Citation(s) in RCA: 152] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Diffusion Monte Carlo studies of water clusters. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1063-5467(98)80012-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Cruzan JD, Viant MR, Brown MG, Saykally RJ. Terahertz Laser Vibration−Rotation Tunneling Spectroscopy of the Water Tetramer. J Phys Chem A 1997. [DOI: 10.1021/jp970782r] [Citation(s) in RCA: 102] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jeff D. Cruzan
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720
| | - Mark R. Viant
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720
| | - Mac G. Brown
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720
| | - Richard J. Saykally
- Department of Chemistry, University of California at Berkeley, Berkeley, California 94720
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Ro/nne C, Thrane L, Åstrand PO, Wallqvist A, Mikkelsen KV, Keiding SR. Investigation of the temperature dependence of dielectric relaxation in liquid water by THz reflection spectroscopy and molecular dynamics simulation. J Chem Phys 1997. [DOI: 10.1063/1.474242] [Citation(s) in RCA: 449] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Nymand TM, Åstrand PO. Electric field-gradient contributions to the chemical shifts of liquid water. J Chem Phys 1997. [DOI: 10.1063/1.473896] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Engkvist O, Karlström G. A Monte Carlo simulation study of the temperature dependence for the conformation distribution of 1,2-dimethoxyethane in water. J Chem Phys 1997. [DOI: 10.1063/1.473152] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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ENGKVIST OLA, FORSBERG NICLAS, SCHUTZ MARTIN, KARLSTROM GUNNAR. A comparison between the NEMO intermolecular water potential and ab initio quantum chemical calculations for the water trimer tetramer. Mol Phys 1997. [DOI: 10.1080/002689797172769] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Sorenson JM, Gregory JK, Clary DC. The C6H6–(H2O)2 complex: Theoretical predictions of the structure, energetics, and tunneling dynamics. J Chem Phys 1997. [DOI: 10.1063/1.473180] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Sorenson JM, Gregory JK, Clary DC. Diffusion Monte Carlo studies of isotope-substituted water trimers. Chem Phys Lett 1996. [DOI: 10.1016/s0009-2614(96)01264-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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